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annotate rsem.xml @ 12:ad708409d25e draft default tip

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"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit fdb6ccd340e366ef386d69ff344036a83e479b2f"
author artbio
date Tue, 03 Mar 2020 12:28:11 +0000
parents c86ed39b72eb
children
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7
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
artbio
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1 <tool id="rsembowtie" name="RSEM-Bowtie" version="@WRAPPER_VERSION@">
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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2 <description></description>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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3 <macros>
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4 <import>macros.xml</import>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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5 </macros>
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c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
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6 <expand macro="requirements" />
0
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7 <stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8 <exit_code range="1:" level="warning" description="Tool exception" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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9 </stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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10 <command detect_errors="exit_code"><![CDATA[
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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11 #if $job.select_job == "index":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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12 echo ${job.reference_name} " " | tee $reference_file &&
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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13 mkdir $reference_file.files_path &&
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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14 rsem-prepare-reference
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15 #if $job.polya.polya_use == 'add':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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16 #if $job.polya.polya_length:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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17 --polyA-length $job.polya.polya_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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18 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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19 #elif $job.polya.polya_use == 'subset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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20 --no-polyA-subset $job.polya.no_polya_subset
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21 #if $job.polya.polya_length:
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22 --polyA-length $job.polya.polya_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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23 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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24 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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25 $job.ntog
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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26 #if $job.transcript_to_gene_map:
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27 --transcript-to-gene-map $job.transcript_to_gene_map
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28 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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29 --bowtie
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30 #if $job.self_reference.ref_type == 'transcripts':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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31 $job.self_reference.reference_fasta_file
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32 #else:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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33 --gtf $job.self_reference.gtf
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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34 $job.self_reference.reference_fasta_file
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35 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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36 ${reference_file.files_path}/${job.reference_name}
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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37 > ${reference_file.files_path}/${job.reference_name}.log
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38 #end if
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39
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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40 #if $job.select_job == "index" and $run_rsem.select == "Yes":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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41 &&
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42 #end if
3
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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43
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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44 #if $run_rsem.select == "Yes":
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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45 ## uncompress fastq.gz or fastqsanger.gz if needed
10
6aba6cca3fab planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
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46 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single":
3
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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47 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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48 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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49 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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50 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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51 #end if
10
6aba6cca3fab planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
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52 #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
4
0fa0c1132a7b planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 3f67b2cf90a5de9880c98a6e492c444a5c856275
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53 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
3
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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54 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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55 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
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c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
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56 #elif $run_rsem.input.fastq.fastq1.is_of_type('fastq') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'):
3
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
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57 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
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58 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
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59 #end if
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60 #end if
0
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61 rsem-calculate-expression
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62 ## --tag string
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63 #if $run_rsem.seedlength:
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64 --seed-length $run_rsem.seedlength
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65 #end if
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66 --forward-prob $run_rsem.forward_prob
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67 #if $run_rsem.rsem_options.fullparams == 'fullset':
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68 ## Fragment info
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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69 #if $run_rsem.rsem_options.fragment_length_mean:
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70 --fragment-length-mean $run_rsem.rsem_options.fragment_length_mean
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71 #end if
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72 #if $run_rsem.rsem_options.fragment_length_min:
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73 --fragment-length-min $run_rsem.rsem_options.fragment_length_min
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74 #end if
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75 #if $run_rsem.rsem_options.fragment_length_sd:
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76 --fragment-length-sd $run_rsem.rsem_options.fragment_length_sd
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77 #end if
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78 #if $run_rsem.rsem_options.fragment_length_max:
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79 --fragment-length-max $run_rsem.rsem_options.fragment_length_max
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80 #end if
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81 ## RSPD
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82 #if $run_rsem.rsem_options.rspd.estimate == 'yes':
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83 --estimate-rspd
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84 #if $run_rsem.rsem_options.rspd.num_rspd_bins:
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85 --num-rspd-bins $run_rsem.rsem_options.rspd.num_rspd_bins
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86 #end if
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87 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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88 ## Calculate 95% credibility intervals and posterior mean estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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89 #if $run_rsem.rsem_options.useci.ci == 'yes':
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artbio
parents:
diff changeset
90 --calc-ci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
91 #if $run_rsem.rsem_options.useci.cimem:
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artbio
parents:
diff changeset
92 --ci-memory $run_rsem.rsem_options.useci.cimem
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artbio
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diff changeset
93 #end if
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artbio
parents:
diff changeset
94 #end if
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artbio
parents:
diff changeset
95 #end if
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96 --num-threads \${GALAXY_SLOTS:-4}
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diff changeset
97 #if $run_rsem.input.format == 'fasta' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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98 ## Bowtie params
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diff changeset
99 #if $run_rsem.input.bowtie_options.bowtie_e:
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artbio
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diff changeset
100 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
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101 #end if
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102 #if $run_rsem.input.bowtie_options.bowtie_m:
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artbio
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103 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
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104 #end if
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105 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
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106 #end if
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107 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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108 ## Bowtie params
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109 #if $run_rsem.input.bowtie_options.bowtie_e:
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110 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
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111 #end if
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112 #if $run_rsem.input.bowtie_options.bowtie_m:
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113 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
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114 #end if
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115 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
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116 #end if
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117 ## Outputs
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118 #if $run_rsem.rsem_outputs.result_bams == 'none':
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119 --no-bam-output
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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120 #elif $run_rsem.rsem_outputs.result_bams == 'default':
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121 --sort-bam-by-coordinate
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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122 #else
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123 --sort-bam-by-coordinate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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124 --output-genome-bam
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125 $run_rsem.rsem_outputs.sampling_for_bam
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126 #end if
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127 ## Input data
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128 #if $run_rsem.input.format=="fastq"
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129 $run_rsem.input.fastq_select
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130 #if $run_rsem.input.fastq.matepair=="single":
3
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131 uncomp_single.fastq
0
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132 #elif $run_rsem.input.fastq.matepair=="paired":
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133 --paired-end
3
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134 uncomp_pair1.fastq
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135 uncomp_pair2.fastq
0
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136 #end if
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137 #elif $run_rsem.input.format=="fasta"
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138 --no-qualities
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139 #if $run_rsem.input.fasta.matepair=="single":
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140 $run_rsem.input.fasta.singlefasta
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141 #elif $run_rsem.input.fasta.matepair=="paired":
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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142 --paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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143 $run_rsem.input.fasta.fasta1
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artbio
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144 $run_rsem.input.fasta.fasta2
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145 #end if
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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146 #end if
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147 ## RSEM reference
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148 #if $run_rsem.reference.refSrc == 'history':
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149 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
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150 #elif $run_rsem.reference.refSrc == 'self':
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151 ${reference_file.files_path}/${job.reference_name}
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152 #end if
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153 ## sample_name: use a hard coded name so we can pull out galaxy outputs
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154 rsem_output
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155 ## direct output into logfile
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156 > $log
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157 #end if
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158 ]]></command>
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159
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160 <inputs>
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161 <conditional name="job">
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162 <param name="select_job" type="select" label="rsem reference">
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163 <option value="index">Build rsem reference</option>
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164 <option value="no-index" selected="true">rsem reference available from history</option>
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165 </param>
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166 <when value="index">
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167 <conditional name="self_reference">
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
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diff changeset
168 <param name="ref_type" type="select" label="Reference source">
0
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169 <option value="transcripts">transcript fasta</option>
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170 <option value="genomic">reference genome and gtf</option>
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171 </param>
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172 <when value="transcripts">
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173 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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diff changeset
174 help="The files should contain the sequences of transcripts."/>
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175 </when>
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parents:
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176 <when value="genomic">
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177 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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artbio
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178 help="The file should contain the sequence of an entire genome."/>
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artbio
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179 <param name="gtf" type="data" format="gtf" label="gtf"
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180 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
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181 </when>
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182 </conditional>
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183 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
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184 <help>
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185 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
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186 The map can be obtained from the UCSC table browser
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187 group: Genes and Gene Prediction Tracks
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188 table: knownIsoforms
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189 Without a map:
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190 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
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191 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
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192 </help>
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193 </param>
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194 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
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195 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
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196 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
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197 </param>
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198 <conditional name="polya">
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199 <param name="polya_use" type="select" label="PolyA ">
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200 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
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201 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
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202 <option value="none">Do not add poly(A) tails to any transcripts</option>
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203 </param>
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204 <when value="add">
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205 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
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206 <validator type="in_range" message="must be positive " min="1"/>
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207 </param>
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208 </when>
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209 <when value="subset">
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210 <param name="no_polya_subset" type="data" format="tabular" optional="true" label="List of transcript IDs (one per line) that should should not have polyA tails added."/>
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211 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
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212 <validator type="in_range" message="must be positive " min="1"/>
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213 </param>
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214 </when>
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215 <when value="none"/>
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216 </conditional>
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217 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowtie uses the automatic N to G conversion to align against all positions in the reference."/>
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218 </when>
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219 <when value="no-index">
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220 </when>
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221 </conditional>
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222
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223 <conditional name="run_rsem">
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224 <param name="select" type="select" label="calculate expression with rsem">
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225 <option value="No">Just build rsem reference for latter rsem profiling</option>
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226 <option value="Yes" selected="true">profile expression with rsem</option>
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227 </param>
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228 <when value="Yes">
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229 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
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230 <conditional name="reference">
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231 <param name="refSrc" type="select" label="RSEM Reference Source">
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232 <option value="history">From your history</option>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
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233 <option value="self">RSEM Reference prepared with this tool</option>
0
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234 </param>
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235 <when value="history">
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236 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
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237 </when>
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238 <when value="self">
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239 </when>
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240 </conditional>
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241 <conditional name="input">
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242 <param name="format" type="select" label="RSEM Input file type">
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243 <option value="fastq">FASTQ</option>
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244 <option value="fasta">FASTA</option>
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245 </param>
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246 <when value="fastq">
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247 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
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248 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
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249 <option value="--solexa-quals">solexa qualities</option>
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250 <option value="--phred64-quals">phred64 qualities</option>
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251 </param>
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252 <conditional name="fastq">
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253 <param name="matepair" type="select" label="Library type">
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254 <option value="single">Single End Reads</option>
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255 <option value="paired">Paired End Reads</option>
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256 </param>
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257 <when value="single">
1
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258 <param name="singlefastq" type="data" format="fastq,fastq.gz" label="FASTQ file" />
0
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259 </when>
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260 <when value="paired">
1
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261 <param name="fastq1" type="data" format="fastq,fastq.gz" label="Read 1 fastq file" />
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262 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Read 2 fastq file" />
0
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263 </when>
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264 </conditional>
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265 <expand macro="bowtie_options"/>
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266 </when>
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267 <when value="fasta">
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268 <conditional name="fasta">
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269 <param name="matepair" type="select" label="Library Type">
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270 <option value="single">Single End Reads</option>
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271 <option value="paired">Paired End Reads</option>
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272 </param>
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273 <when value="single">
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274 <param name="singlefasta" type="data" format="fasta" label="fasta file" />
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275 </when>
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276 <when value="paired">
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277 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
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278 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
279 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
280 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
281 <expand macro="bowtie_options"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
282 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
283 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
284 <expand macro="rsem_options"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
285 <conditional name="rsem_outputs">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
286 <param name="result_bams" type="select" label="Create bam results files"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
287 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
288 <option value="none">No BAM results files</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
289 <option value="default" selected="true">Transcript BAM results file</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
290 <option value="both">Transcript and genome BAM results files</option>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
291 </param>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
292 <when value="none"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
293 <when value="default">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
294 <expand macro="sampling_for_bam"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
295 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
296 <when value="both">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
297 <expand macro="sampling_for_bam"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
298 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
299 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
300 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
301 <when value="No">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
302 </when>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
303 </conditional>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
304 </inputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
305
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
306 <outputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
307 <data format="rsem_ref" name="reference_file" label="RSEM ${job.reference_name} reference">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
308 <filter>job['select_job'] == "index"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
309 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
310 <data format="tabular" name="gene_abundances" label="${run_rsem.sample}.gene_abundances" from_work_dir="rsem_output.genes.results">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
311 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
312 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
313 <data format="tabular" name="isoform_abundances" label="${run_rsem.sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
314 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
315 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
316 <data format="bam" name="transcript_sorted_bam" label="${run_rsem.sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents: 4
diff changeset
317 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] != "none"</filter>
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
318 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
319 <data format="bam" name="genome_sorted_bam" label="${run_rsem.sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents: 4
diff changeset
320 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] == "both"</filter>
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
321 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
322 <data format="txt" name="log" label="${run_rsem.sample}.rsem_log">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
323 <filter>run_rsem['select'] == "Yes"</filter>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
324 </data>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
325 </outputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
326
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
327 <tests>
3
9c7c44935bf1 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit ac6ef17eaa8d0eb3a2e681be97b24049d7a7aa22
artbio
parents: 2
diff changeset
328 <test>
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
329 <param name="select_job" value="index"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
330 <param name="ref_type" value="genomic"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
331 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
332 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
333 <param name="reference_name" value="ebola"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
334 <param name="select" value="Yes"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
335 <param name="sample" value="ebola_RNAseq"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
336 <param name="refSrc" value="self"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
337 <param name="format" value="fastq"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
338 <param name="matepair" value="single"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
339 <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
340 <param name="result_bams" value="none"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
341 <output name="reference_file">
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
342 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
343 <has_text text="ebola" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
344 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
345 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
346 <output name="gene_abundances" value="refgen_gene_abundances.bt.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
347 <output name="isoform_abundances" value="refgen_isoform_abundances.bt.tab" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
348 <output name="log">
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
349 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
350 <has_text text="Expression Results are written" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
351 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
352 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
353 </test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
354 <test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
355 <!-- test fastqsanger paired end Ebola genome-->
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
356 <param name="select_job" value="index"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
357 <param name="ref_type" value="genomic"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
358 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
359 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
360 <param name="reference_name" value="ebola"/>
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
361 <param name="select" value="Yes"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
362 <param name="sample" value="rsem_sample"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
363 <param name="refSrc" value="self"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
364 <param name="format" value="fastq"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
365 <param name="matepair" value="paired"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
366 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
367 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
368 <param name="result_bams" value="both" />
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
369 <output name="reference_file">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
370 <assert_contents>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
371 <has_text text="ebola" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
372 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
373 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
374 <output name="gene_abundances" value="paired_refgen_gene_abundances.bt.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
375 <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt.tab" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
376 <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt.bam" ftype="bam" lines_diff="4" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
377 <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt.bam" ftype="bam" lines_diff="4" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
378 <output name="log">
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
379 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
380 <has_text text="Expression Results are written" />
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
381 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
382 </output>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
383 </test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
384 <test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
385 <!-- test fastqsanger paired end Ebola transcripts -->
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
386 <param name="select_job" value="index"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
387 <param name="ref_type" value="transcripts"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
388 <param name="reference_fasta_file" value="Ebola_transcripts.fa" ftype="fasta"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
389 <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="tabular"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
390 <param name="reference_name" value="ebola"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
391 <param name="select" value="Yes"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
392 <param name="sample" value="rsem_sample"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
393 <param name="refSrc" value="self"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
394 <param name="format" value="fastq"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
395 <param name="matepair" value="paired"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
396 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
397 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
398 <param name="result_bams" value="default" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
399 <output name="reference_file">
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
400 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
401 <has_text text="ebola" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
402 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
403 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
404 <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
405 <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt.tab" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
406 <output name="transcript_sorted_bam" value="paired_reftrans_transcripts.bt.bam" ftype="bam" lines_diff="2" />
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
407 <output name="log">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
408 <assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
409 <has_text text="Expression Results are written" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
410 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
411 </output>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
412 </test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
413 <test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
414 <param name="select_job" value="index"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
415 <param name="ref_type" value="genomic"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
416 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
417 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
418 <param name="reference_name" value="ebola"/>
1
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
419 <param name="select" value="Yes"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
420 <param name="sample" value="rsem_sample"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
421 <param name="refSrc" value="self"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
422 <param name="format" value="fastq"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
423 <param name="matepair" value="single"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
424 <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
1
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
425 <param name="result_bams" value="none"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
426 <output name="reference_file">
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
427 <assert_contents>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
428 <has_text text="ebola" />
1
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
429 </assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
430 </output>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
431 <output name="gene_abundances" value="single_refgen_gene_abundances.bt.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
432 <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt.tab" />
1
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
433 <output name="log">
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
434 <assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
435 <has_text text="Expression Results are written" />
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
436 </assert_contents>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
437 </output>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
438 </test>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
439 <test>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
440 <param name="select_job" value="index"/>
f9f98166eff8 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
artbio
parents: 0
diff changeset
441 <param name="ref_type" value="genomic"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
442 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
443 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
444 <param name="reference_name" value="alone"/>
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
445 <param name="select" value="No"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
446 <output name="reference_file">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
447 <assert_contents>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
448 <has_text text="alone" />
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
449 </assert_contents>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
450 </output>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
451 </test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
452 </tests>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
453
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
454 <help>
6
39b8e13b1fc9 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f01c120abce1894ac9c6b298d301d4a2c740fc67
artbio
parents: 5
diff changeset
455 .. class:: infomark
0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
456
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
457 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
458
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
459 NAME
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
460 rsem-prepare-reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
461
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
462 SYNOPSIS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
463 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
464
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
465 DESCRIPTION
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
466 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
467 This program is used in conjunction with the 'rsem-calculate-expression' program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
468
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
469 INPUTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
470 A fasta file of transcripts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
471 or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
472 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
473
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
474 ---
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
475
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
476 NAME
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
477 rsem-calculate-expression - Estimate gene and isoform expression from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
478 RNA-Seq data.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
479
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
480 SYNOPSIS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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481 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
482 rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
483 rsem-calculate-expression [options] --alignments [--paired-end] input reference_name sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
484
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
485 ARGUMENTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
486 upstream_read_files(s)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
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diff changeset
487 Comma-separated list of files containing single-end reads or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
488 upstream reads for paired-end data. By default, these files are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
489 assumed to be in FASTQ format. If the --no-qualities option is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
490 specified, then FASTA format is expected.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
491
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
492 downstream_read_file(s)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
493 Comma-separated list of files containing downstream reads which are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
494 paired with the upstream reads. By default, these files are assumed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
495 to be in FASTQ format. If the --no-qualities option is specified,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
496 then FASTA format is expected.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
497
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
498 input
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
499 SAM/BAM/CRAM formatted input file. If "-" is specified for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
500 filename, the input is instead assumed to come from standard input.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
501 RSEM requires all alignments of the same read group together. For
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
502 paired-end reads, RSEM also requires the two mates of any alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
503 be adjacent. In addition, RSEM does not allow the SEQ and QUAL
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
504 fields to be empty. See Description section for how to make input
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
505 file obey RSEM's requirements.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
506
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
507 reference_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
508 The name of the reference used. The user must have run
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
509 'rsem-prepare-reference' with this reference_name before running
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
510 this program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
511
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
512 sample_name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
513 The name of the sample analyzed. All output files are prefixed by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
514 this name (e.g., sample_name.genes.results)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
515
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
516 BASIC OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
517 --paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
518 Input reads are paired-end reads. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
519
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
520 --no-qualities
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
521 Input reads do not contain quality scores. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
522
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
523 --strandedness &lt;none|forward|reverse&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
524 This option defines the strandedness of the RNA-Seq reads. It
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
525 recognizes three values: 'none', 'forward', and 'reverse'. 'none'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
526 refers to non-strand-specific protocols. 'forward' means all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
527 (upstream) reads are derived from the forward strand. 'reverse'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
528 means all (upstream) reads are derived from the reverse strand. If
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
529 'forward'/'reverse' is set, the '--norc'/'--nofw' Bowtie/Bowtie 2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
530 option will also be enabled to avoid aligning reads to the opposite
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
531 strand. For Illumina TruSeq Stranded protocols, please use
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
532 'reverse'. (Default: 'none')
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
533
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
534 -p/--num-threads &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
535 Number of threads to use. Both Bowtie/Bowtie2, expression estimation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
536 and 'samtools sort' will use this many threads. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
537
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
538 --alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
539 Input file contains alignments in SAM/BAM/CRAM format. The exact
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
540 file format will be determined automatically. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
541
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
542 --fai &lt;file&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
543 If the header section of input alignment file does not contain
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
544 reference sequence information, this option should be turned on.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
545 &lt;file&gt; is a FAI format file containing each reference sequence's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
546 name and length. Please refer to the SAM official website for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
547 details of FAI format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
548
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
549 --bowtie2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
550 Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
551 does not handle indel, local and discordant alignments, the Bowtie2
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
552 parameters are set in a way to avoid those alignments. In
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
553 particular, we use options '--sensitive --dpad 0 --gbar 99999999
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
554 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. The last parameter
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
555 of '--score-min', '-0.1', is the negative of maximum mismatch rate.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
556 This rate can be set by option '--bowtie2-mismatch-rate'. If reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
557 are paired-end, we additionally use options '--no-mixed' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
558 '--no-discordant'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
559
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
560 --star
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
561 Use STAR to align reads. Alignment parameters are from ENCODE3's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
562 STAR-RSEM pipeline. To save computational time and memory resources,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
563 STAR's Output BAM file is unsorted. It is stored in RSEM's temporary
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
564 directory with name as 'sample_name.bam'. Each STAR job will have
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
565 its own private copy of the genome in memory. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
566
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
567 --append-names
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
568 If gene_name/transcript_name is available, append it to the end of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
569 gene_id/transcript_id (separated by '_') in files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
570 'sample_name.isoforms.results' and 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
571 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
572
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
573 --seed &lt;uint32&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
574 Set the seed for the random number generators used in calculating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
575 posterior mean estimates and credibility intervals. The seed must be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
576 a non-negative 32 bit integer. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
577
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
578 --single-cell-prior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
579 By default, RSEM uses Dirichlet(1) as the prior to calculate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
580 posterior mean estimates and credibility intervals. However, much
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
581 less genes are expressed in single cell RNA-Seq data. Thus, if you
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
582 want to compute posterior mean estimates and/or credibility
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
583 intervals and you have single-cell RNA-Seq data, you are recommended
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
584 to turn on this option. Then RSEM will use Dirichlet(0.1) as the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
585 prior which encourage the sparsity of the expression levels.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
586 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
587
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
588 --calc-pme
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
589 Run RSEM's collapsed Gibbs sampler to calculate posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
590 estimates. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
591
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
592 --calc-ci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
593 Calculate 95% credibility intervals and posterior mean estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
594 The credibility level can be changed by setting
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
595 '--ci-credibility-level'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
596
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
597 -q/--quiet
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
598 Suppress the output of logging information. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
599
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
600 -h/--help
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
601 Show help information.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
602
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
603 --version
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
604 Show version information.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
605
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
606 OUTPUT OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
607 --sort-bam-by-read-name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
608 Sort BAM file aligned under transcript coordidate by read name.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
609 Setting this option on will produce deterministic maximum likelihood
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
610 estimations from independent runs. Note that sorting will take long
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
611 time and lots of memory. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
612
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
613 --no-bam-output
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
614 Do not output any BAM file. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
615
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
616 --sampling-for-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
617 When RSEM generates a BAM file, instead of outputting all alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
618 a read has with their posterior probabilities, one alignment is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
619 sampled according to the posterior probabilities. The sampling
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
620 procedure includes the alignment to the "noise" transcript, which
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
621 does not appear in the BAM file. Only the sampled alignment has a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
622 weight of 1. All other alignments have weight 0. If the "noise"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
623 transcript is sampled, all alignments appeared in the BAM file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
624 should have weight 0. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
625
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
626 --output-genome-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
627 Generate a BAM file, 'sample_name.genome.bam', with alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
628 mapped to genomic coordinates and annotated with their posterior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
629 probabilities. In addition, RSEM will call samtools (included in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
630 RSEM package) to sort and index the bam file.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
631 'sample_name.genome.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
632 'sample_name.genome.sorted.bam.bai' will be generated. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
633 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
634
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
635 --sort-bam-by-coordinate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
636 Sort RSEM generated transcript and genome BAM files by coordinates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
637 and build associated indices. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
638
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
639 --sort-bam-memory-per-thread &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
640 Set the maximum memory per thread that can be used by 'samtools
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
641 sort'. &lt;string&gt; represents the memory and accepts suffices 'K/M/G'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
642 RSEM will pass &lt;string&gt; to the '-m' option of 'samtools sort'. Note
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
643 that the default used here is different from the default used by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
644 samtools. (Default: 1G)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
645
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
646 ALIGNER OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
647 --seed-length &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
648 Seed length used by the read aligner. Providing the correct value is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
649 important for RSEM. If RSEM runs Bowtie, it uses this value for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
650 Bowtie's seed length parameter. Any read with its or at least one of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
651 its mates' (for paired-end reads) length less than this value will
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
652 be ignored. If the references are not added poly(A) tails, the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
653 minimum allowed value is 5, otherwise, the minimum allowed value is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
654 25. Note that this script will only check if the value &gt;= 5 and give
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
655 a warning message if the value &lt; 25 but &gt;= 5. (Default: 25)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
656
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
657 --phred33-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
658 Input quality scores are encoded as Phred+33. (Default: on)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
659
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
660 --phred64-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
661 Input quality scores are encoded as Phred+64 (default for GA
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
662 Pipeline ver. &gt;= 1.3). (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
663
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
664 --solexa-quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
665 Input quality scores are solexa encoded (from GA Pipeline ver. &lt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
666 1.3). (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
667
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
668 --bowtie-path &lt;path&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
669 The path to the Bowtie executables. (Default: the path to the Bowtie
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
670 executables is assumed to be in the user's PATH environment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
671 variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
672
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
673 --bowtie-n &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
674 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
675 Default: 2)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
676
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
677 --bowtie-e &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
678 (Bowtie parameter) max sum of mismatch quality scores across the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
679 alignment. (Default: 99999999)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
680
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
681 --bowtie-m &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
682 (Bowtie parameter) suppress all alignments for a read if &gt; &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
683 valid alignments exist. (Default: 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
684
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
685 --bowtie-chunkmbs &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
686 (Bowtie parameter) memory allocated for best first alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
687 calculation (Default: 0 - use Bowtie's default)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
688
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
689 --bowtie2-path &lt;path&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
690 (Bowtie 2 parameter) The path to the Bowtie 2 executables. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
691 the path to the Bowtie 2 executables is assumed to be in the user's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
692 PATH environment variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
693
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
694 --bowtie2-mismatch-rate &lt;double&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
695 (Bowtie 2 parameter) The maximum mismatch rate allowed. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
696 0.1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
697
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
698 --bowtie2-k &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
699 (Bowtie 2 parameter) Find up to &lt;int&gt; alignments per read. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
700 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
701
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
702 --bowtie2-sensitivity-level &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
703 (Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
704 mode. This option controls how hard Bowtie 2 tries to find
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
705 alignments. &lt;string&gt; must be one of "very_fast", "fast", "sensitive"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
706 and "very_sensitive". The four candidates correspond to Bowtie 2's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
707 "--very-fast", "--fast", "--sensitive" and "--very-sensitive"
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
708 options. (Default: "sensitive" - use Bowtie 2's default)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
709
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
710 --star-path &lt;path&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
711 The path to STAR's executable. (Default: the path to STAR executable
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
712 is assumed to be in user's PATH environment variable)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
713
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
714 --star-gzipped-read-file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
715 (STAR parameter) Input read file(s) is compressed by gzip. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
716 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
717
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
718 --star-bzipped-read-file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
719 (STAR parameter) Input read file(s) is compressed by bzip2.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
720 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
721
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
722 --star-output-genome-bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
723 (STAR parameter) Save the BAM file from STAR alignment under genomic
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
724 coordinate to 'sample_name.STAR.genome.bam'. This file is NOT sorted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
725 by genomic coordinate. In this file, according to STAR's manual,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
726 'paired ends of an alignment are always adjacent, and multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
727 alignments of a read are adjacent as well'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
728
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
729 ADVANCED OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
730 --tag &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
731 The name of the optional field used in the SAM input for identifying
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
732 a read with too many valid alignments. The field should have the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
733 format &lt;tagName&gt;:i:&lt;value&gt;, where a &lt;value&gt; bigger than 0 indicates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
734 a read with too many alignments. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
735
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
736 --fragment-length-min &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
737 Minimum read/insert length allowed. This is also the value for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
738 Bowtie/Bowtie2 -I option. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
739
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
740 --fragment-length-max &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
741 Maximum read/insert length allowed. This is also the value for the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
742 Bowtie/Bowtie 2 -X option. (Default: 1000)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
743
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
744 --fragment-length-mean &lt;double&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
745 (single-end data only) The mean of the fragment length distribution,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
746 which is assumed to be a Gaussian. (Default: -1, which disables use
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
747 of the fragment length distribution)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
748
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
749 --fragment-length-sd &lt;double&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
750 (single-end data only) The standard deviation of the fragment length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
751 distribution, which is assumed to be a Gaussian. (Default: 0, which
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
752 assumes that all fragments are of the same length, given by the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
753 rounded value of --fragment-length-mean)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
754
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
755 --estimate-rspd
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
756 Set this option if you want to estimate the read start position
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
757 distribution (RSPD) from data. Otherwise, RSEM will use a uniform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
758 RSPD. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
759
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
760 --num-rspd-bins &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
761 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
762 specified. Use of the default setting is recommended. (Default: 20)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
763
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
764 --gibbs-burnin &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
765 The number of burn-in rounds for RSEM's Gibbs sampler. Each round
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
766 passes over the entire data set once. If RSEM can use multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
767 threads, multiple Gibbs samplers will start at the same time and all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
768 samplers share the same burn-in number. (Default: 200)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
769
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
770 --gibbs-number-of-samples &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
771 The total number of count vectors RSEM will collect from its Gibbs
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
772 samplers. (Default: 1000)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
773
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
774 --gibbs-sampling-gap &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
775 The number of rounds between two succinct count vectors RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
776 collects. If the count vector after round N is collected, the count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
777 vector after round N + &lt;int&gt; will also be collected. (Default: 1)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
778
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
779 --ci-credibility-level &lt;double&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
780 The credibility level for credibility intervals. (Default: 0.95)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
781
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
782 --ci-memory &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
783 Maximum size (in memory, MB) of the auxiliary buffer used for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
784 computing credibility intervals (CI). (Default: 1024)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
785
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
786 --ci-number-of-samples-per-count-vector &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
787 The number of read generating probability vectors sampled per
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
788 sampled count vector. The crebility intervals are calculated by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
789 first sampling P(C | D) and then sampling P(Theta | C) for each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
790 sampled count vector. This option controls how many Theta vectors
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
791 are sampled per sampled count vector. (Default: 50)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
792
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
793 --keep-intermediate-files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
794 Keep temporary files generated by RSEM. RSEM creates a temporary
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
795 directory, 'sample_name.temp', into which it puts all intermediate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
796 output files. If this directory already exists, RSEM overwrites all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
797 files generated by previous RSEM runs inside of it. By default,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
798 after RSEM finishes, the temporary directory is deleted. Set this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
799 option to prevent the deletion of this directory and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
800 intermediate files inside of it. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
801
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
802 --temporary-folder &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
803 Set where to put the temporary files generated by RSEM. If the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
804 folder specified does not exist, RSEM will try to create it.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
805 (Default: sample_name.temp)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
806
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
807 --time
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
808 Output time consumed by each step of RSEM to 'sample_name.time'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
809 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
810
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
811 PRIOR-ENHANCED RSEM OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
812 --run-pRSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
813 Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
814 isoform's initial pseudo-count for RSEM's Gibbs sampling, will be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
815 learned from input RNA-seq data and an external data set. When pRSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
816 needs and only needs ChIP-seq peak information to partition isoforms
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
817 (e.g. in pRSEM's default partition model), either ChIP-seq peak file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
818 (with the '--chipseq-peak-file' option) or ChIP-seq FASTQ files for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
819 target and input and the path for Bowtie executables are required
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
820 (with the '--chipseq-target-read-files &lt;string&gt;',
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
821 '--chipseq-control-read-files &lt;string&gt;', and '--bowtie-path &lt;path&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
822 options), otherwise, ChIP-seq FASTQ files for target and control and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
823 the path to Bowtie executables are required. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
824
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
825 --chipseq-peak-file &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
826 Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
827 BED6+4, format. This file is used when running prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
828 in the default two-partition model. It partitions isoforms by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
829 whether they have ChIP-seq overlapping with their transcription
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
830 start site region or not. Each partition will have its own prior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
831 parameter learned from a training set. This file can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
832 gzipped or ungzipped. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
833
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
834 --chipseq-target-read-files &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
835 Comma-separated full path of FASTQ read file(s) for ChIP-seq target.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
836 This option is used when running prior-enhanced RSEM. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
837 information to calculate ChIP-seq peaks and signals. The file(s) can
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
838 be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
839 options '--bowtie-path &lt;path&gt;' and '--chipseq-control-read-files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
840 &lt;string&gt;' must be defined when this option is specified. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
841 "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
842
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
843 --chipseq-control-read-files &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
844 Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
845 This option is used when running prior-enhanced RSEM. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
846 information to call ChIP-seq peaks. The file(s) can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
847 ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
848 '--bowtie-path &lt;path&gt;' and '--chipseq-target-read-files &lt;string&gt;'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
849 must be defined when this option is specified. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
850
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
851 --chipseq-read-files-multi-targets &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
852 Comma-separated full path of FASTQ read files for multiple ChIP-seq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
853 targets. This option is used when running prior-enhanced RSEM, where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
854 prior is learned from multiple complementary data sets. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
855 information to calculate ChIP-seq signals. All files can be either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
856 ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
857 option is specified, the option '--bowtie-path &lt;path&gt;' must be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
858 defined and the option '--partition-model &lt;string&gt;' will be set to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
859 'cmb_lgt' automatically. (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
860
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
861 --chipseq-bed-files-multi-targets &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
862 Comma-separated full path of BED files for multiple ChIP-seq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
863 targets. This option is used when running prior-enhanced RSEM, where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
864 prior is learned from multiple complementary data sets. It provides
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
865 information of ChIP-seq signals and must have at least the first six
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
866 BED columns. All files can be either ungzipped or gzipped with a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
867 suffix '.gz' or '.gzip'. When this option is specified, the option
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
868 '--partition-model &lt;string&gt;' will be set to 'cmb_lgt' automatically.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
869 (Default: "")
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
870
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
871 --cap-stacked-chipseq-reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
872 Keep a maximum number of ChIP-seq reads that aligned to the same
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
873 genomic interval. This option is used when running prior-enhanced
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
874 RSEM, where prior is learned from multiple complementary data sets.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
875 This option is only in use when either
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
876 '--chipseq-read-files-multi-targets &lt;string&gt;' or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
877 '--chipseq-bed-files-multi-targets &lt;string&gt;' is specified. (Default:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
878 off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
879
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
880 --n-max-stacked-chipseq-reads &lt;int&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
881 The maximum number of stacked ChIP-seq reads to keep. This option is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
882 used when running prior-enhanced RSEM, where prior is learned from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
883 multiple complementary data sets. This option is only in use when
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
884 the option '--cap-stacked-chipseq-reads' is set. (Default: 5)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
885
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
886 --partition-model &lt;string&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
887 A keyword to specify the partition model used by prior-enhanced
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
888 RSEM. It must be one of the following keywords:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
889
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
890 - pk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
891 Partitioned by whether an isoform has a ChIP-seq peak overlapping
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
892 with its transcription start site (TSS) region. The TSS region is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
893 defined as [TSS-500bp, TSS+500bp]. For simplicity, we refer this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
894 type of peak as 'TSS peak' when explaining other keywords.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
895
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
896 - pk_lgtnopk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
897 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
898 peak' set, a logistic model is employed to further classify them
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
899 into two partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
900
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
901 - lm3, lm4, lm5, or lm6
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
902 Based on their ChIP-seq signals, isoforms are classified into 3,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
903 4, 5, or 6 partitions by a linear regression model.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
904
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
905 - nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
906 First partitioned by TSS peak. Then, for isoforms in the 'with TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
907 peak' set, a linear regression model is employed to further
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
908 classify them into 2, 3, 4, or 5 partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
909
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
910 - pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
911 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
912 peak' set, a linear regression model is employed to further
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
913 classify them into 2, 3, 4, or 5 partitions.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
914
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
915 - cmb_lgt
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
916 Using a logistic regression to combine TSS signals from multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
917 complementary data sets and partition training set isoform into
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
918 'expressed' and 'not expressed'. This partition model is only in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
919 use when either '--chipseq-read-files-multi-targets &lt;string&gt;' or
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
920 '--chipseq-bed-files-multi-targets &lt;string&gt; is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
921
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
922 Parameters for all the above models are learned from a training set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
923 For detailed explanations, please see prior-enhanced RSEM's paper.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
924 (Default: 'pk')
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
925
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
926 DEPRECATED OPTIONS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
927 The options in this section are deprecated. They are here only for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
928 compatibility reasons and may be removed in future releases.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
929
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
930 --sam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
931 Inputs are alignments in SAM format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
932
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
933 --bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
934 Inputs are alignments in BAM format. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
935
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
936 --strand-specific
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
937 Equivalent to '--strandedness forward'. (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
938
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
939 --forward-prob &lt;double&gt;
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
940 Probability of generating a read from the forward strand of a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
941 transcript. Set to 1 for a strand-specific protocol where all
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
942 (upstream) reads are derived from the forward strand, 0 for a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
943 strand-specific protocol where all (upstream) read are derived from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
944 the reverse strand, or 0.5 for a non-strand-specific protocol.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
945 (Default: off)
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
946
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
947 DESCRIPTION
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
948 In its default mode, this program aligns input reads against a reference
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
949 transcriptome with Bowtie and calculates expression values using the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
950 alignments. RSEM assumes the data are single-end reads with quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
951 scores, unless the '--paired-end' or '--no-qualities' options are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
952 specified. Alternatively, users can use STAR to align reads using the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
953 '--star' option. RSEM has provided options in 'rsem-prepare-reference'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
954 to prepare STAR's genome indices. Users may use an alternative aligner
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
955 by specifying '--alignments', and providing an alignment file in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
956 SAM/BAM/CRAM format. However, users should make sure that they align
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
957 against the indices generated by 'rsem-prepare-reference' and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
958 alignment file satisfies the requirements mentioned in ARGUMENTS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
959 section.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
960
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
961 One simple way to make the alignment file satisfying RSEM's requirements
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
962 is to use the 'convert-sam-for-rsem' script. This script accepts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
963 SAM/BAM/CRAM files as input and outputs a BAM file. For example, type
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
964 the following command to convert a SAM file, 'input.sam', to a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
965 ready-for-use BAM file, 'input_for_rsem.bam':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
966
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
967 convert-sam-for-rsem input.sam input_for_rsem
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
968
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
969 For details, please refer to 'convert-sam-for-rsem's documentation page.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
970
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
971 NOTES
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
972 1. Users must run 'rsem-prepare-reference' with the appropriate
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
973 reference before using this program.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
974
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
975 2. For single-end data, it is strongly recommended that the user provide
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
976 the fragment length distribution parameters (--fragment-length-mean and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
977 --fragment-length-sd). For paired-end data, RSEM will automatically
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
978 learn a fragment length distribution from the data.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
979
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
980 3. Some aligner parameters have default values different from their
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
981 original settings.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
982
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
983 4. With the '--calc-pme' option, posterior mean estimates will be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
984 calculated in addition to maximum likelihood estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
985
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
986 5. With the '--calc-ci' option, 95% credibility intervals and posterior
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
987 mean estimates will be calculated in addition to maximum likelihood
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
988 estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
989
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
990 6. The temporary directory and all intermediate files will be removed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
991 when RSEM finishes unless '--keep-intermediate-files' is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
992
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
993 With the '--run-pRSEM' option and associated options (see section
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
994 'PRIOR-ENHANCED RSEM OPTIONS' above for details), prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
995 will be running. Prior parameters will be learned from supplied external
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
996 data set(s) and assigned as initial pseudo-counts for isoforms in the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
997 corresponding partition for Gibbs sampling.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
998
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
999 OUTPUT
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1000 sample_name.isoforms.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1001 File containing isoform level expression estimates. The first line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1002 contains column names separated by the tab character. The format of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1003 each line in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1004
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1005 transcript_id gene_id length effective_length expected_count TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1006 FPKM IsoPct [posterior_mean_count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1007 posterior_standard_deviation_of_count pme_TPM pme_FPKM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1008 IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1009 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1010 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1011
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1012 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1013 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1014 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1015
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1016 'transcript_id' is the transcript name of this transcript. 'gene_id'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1017 is the gene name of the gene which this transcript belongs to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1018 (denote this gene as its parent gene). If no gene information is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1019 provided, 'gene_id' and 'transcript_id' are the same.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1020
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1021 'length' is this transcript's sequence length (poly(A) tail is not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1022 counted). 'effective_length' counts only the positions that can
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1023 generate a valid fragment. If no poly(A) tail is added,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1024 'effective_length' is equal to transcript length - mean fragment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1025 length + 1. If one transcript's effective length is less than 1,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1026 this transcript's both effective length and abundance estimates are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1027 set to 0.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1028
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1029 'expected_count' is the sum of the posterior probability of each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1030 read comes from this transcript over all reads. Because 1) each read
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1031 aligning to this transcript has a probability of being generated
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1032 from background noise; 2) RSEM may filter some alignable low quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1033 reads, the sum of expected counts for all transcript are generally
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1034 less than the total number of reads aligned.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1035
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1036 'TPM' stands for Transcripts Per Million. It is a relative measure
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1037 of transcript abundance. The sum of all transcripts' TPM is 1
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1038 million. 'FPKM' stands for Fragments Per Kilobase of transcript per
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1039 Million mapped reads. It is another relative measure of transcript
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1040 abundance. If we define l_bar be the mean transcript length in a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1041 sample, which can be calculated as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1042
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1043 l_bar = \sum_i TPM_i / 10^6 * effective_length_i (i goes through
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1044 every transcript),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1045
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1046 the following equation is hold:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1047
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1048 FPKM_i = 10^3 / l_bar * TPM_i.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1049
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1050 We can see that the sum of FPKM is not a constant across samples.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1051
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1052 'IsoPct' stands for isoform percentage. It is the percentage of this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1053 transcript's abandunce over its parent gene's abandunce. If its
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1054 parent gene has only one isoform or the gene information is not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1055 provided, this field will be set to 100.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1056
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1057 'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1058 estimates calculated by RSEM's Gibbs sampler.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1059 'posterior_standard_deviation_of_count' is the posterior standard
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1060 deviation of counts. 'IsoPct_from_pme_TPM' is the isoform percentage
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1061 calculated from 'pme_TPM' values.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1062
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1063 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1064 and 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1065 credibility intervals for TPM and FPKM values. The bounds are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1066 inclusive (i.e. [l, u]).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1067
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1068 'TPM_coefficient_of_quartile_variation' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1069 'FPKM_coefficient_of_quartile_variation' are coefficients of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1070 quartile variation (CQV) for TPM and FPKM values. CQV is a robust
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1071 way of measuring the ratio between the standard deviation and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1072 mean. It is defined as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1073
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1074 CQV := (Q3 - Q1) / (Q3 + Q1),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1075
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1076 where Q1 and Q3 are the first and third quartiles.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1077
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1078 sample_name.genes.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1079 File containing gene level expression estimates. The first line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1080 contains column names separated by the tab character. The format of
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1081 each line in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1082
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1083 gene_id transcript_id(s) length effective_length expected_count TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1084 FPKM [posterior_mean_count posterior_standard_deviation_of_count
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1085 pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1086 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1087 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1088
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1089 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1090 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1091 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1092
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1093 'transcript_id(s)' is a comma-separated list of transcript_ids
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1094 belonging to this gene. If no gene information is provided,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1095 'gene_id' and 'transcript_id(s)' are identical (the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1096 'transcript_id').
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1097
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1098 A gene's 'length' and 'effective_length' are defined as the weighted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1099 average of its transcripts' lengths and effective lengths (weighted
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1100 by 'IsoPct'). A gene's abundance estimates are just the sum of its
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1101 transcripts' abundance estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1102
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1103 sample_name.alleles.results
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1104 Only generated when the RSEM references are built with
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1105 allele-specific transcripts.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1106
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1107 This file contains allele level expression estimates for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1108 allele-specific expression calculation. The first line contains
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1109 column names separated by the tab character. The format of each line
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1110 in the rest of this file is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1111
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1112 allele_id transcript_id gene_id length effective_length
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1113 expected_count TPM FPKM AlleleIsoPct AlleleGenePct
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1114 [posterior_mean_count posterior_standard_deviation_of_count pme_TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1115 pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1116 TPM_ci_lower_bound TPM_ci_upper_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1117 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1118 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1119
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1120 Fields are separated by the tab character. Fields within "[]" are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1121 optional. They will not be presented if neither '--calc-pme' nor
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1122 '--calc-ci' is set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1123
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1124 'allele_id' is the allele-specific name of this allele-specific
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1125 transcript.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1126
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1127 'AlleleIsoPct' stands for allele-specific percentage on isoform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1128 level. It is the percentage of this allele-specific transcript's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1129 abundance over its parent transcript's abundance. If its parent
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1130 transcript has only one allele variant form, this field will be set
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1131 to 100.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1132
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1133 'AlleleGenePct' stands for allele-specific percentage on gene level.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1134 It is the percentage of this allele-specific transcript's abundance
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1135 over its parent gene's abundance.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1136
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1137 'AlleleIsoPct_from_pme_TPM' and 'AlleleGenePct_from_pme_TPM' have
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1138 similar meanings. They are calculated based on posterior mean
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1139 estimates.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1140
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1141 Please note that if this file is present, the fields 'length' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1142 'effective_length' in 'sample_name.isoforms.results' should be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1143 interpreted similarly as the corresponding definitions in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1144 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1145
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1146 sample_name.transcript.bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1147 Only generated when --no-bam-output is not specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1148
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1149 'sample_name.transcript.bam' is a BAM-formatted file of read
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1150 alignments in transcript coordinates. The MAPQ field of each
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1151 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1152 where w is the posterior probability of that alignment being the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1153 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1154 where value is a single precision floating number representing the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1155 posterior probability. Because this file contains all alignment
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1156 lines produced by bowtie or user-specified aligners, it can also be
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1157 used as a replacement of the aligner generated BAM/SAM file.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1158
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1159 sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1160 Only generated when --no-bam-output is not specified and --sort-bam-by-coordinate is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1161
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1162 'sample_name.transcript.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1163 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1164 indices generated by samtools (included in RSEM package).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1165
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1166 sample_name.genome.bam
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1167 Only generated when --no-bam-output is not specified and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1168 --output-genome-bam is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1169
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1170 'sample_name.genome.bam' is a BAM-formatted file of read alignments
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1171 in genomic coordinates. Alignments of reads that have identical
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1172 genomic coordinates (i.e., alignments to different isoforms that
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1173 share the same genomic region) are collapsed into one alignment. The
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1174 MAPQ field of each alignment is set to min(100, floor(-10 *
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1175 log10(1.0 - w) + 0.5)), where w is the posterior probability of that
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1176 alignment being the true mapping of a read. In addition, RSEM pads a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1177 new tag ZW:f:value, where value is a single precision floating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1178 number representing the posterior probability. If an alignment is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1179 spliced, a XS:A:value tag is also added, where value is either '+'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1180 or '-' indicating the strand of the transcript it aligns to.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1181
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1182 sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1183 Only generated when --no-bam-output is not specified, and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1184 --sort-bam-by-coordinate and --output-genome-bam are specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1185
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1186 'sample_name.genome.sorted.bam' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1187 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1188 indices generated by samtools (included in RSEM package).
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1189
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1190 sample_name.time
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1191 Only generated when --time is specified.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1192
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1193 It contains time (in seconds) consumed by aligning reads, estimating
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1194 expression levels and calculating credibility intervals.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1195
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1196 sample_name.stat
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1197 This is a folder instead of a file. All model related statistics are
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1198 stored in this folder. Use 'rsem-plot-model' can generate plots
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1199 using this folder.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1200
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1201 'sample_name.stat/sample_name.cnt' contains alignment statistics.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1202 The format and meanings of each field are described in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1203 'cnt_file_description.txt' under RSEM directory.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1204
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1205 'sample_name.stat/sample_name.model' stores RNA-Seq model parameters
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1206 learned from the data. The format and meanings of each filed of this
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1207 file are described in 'model_file_description.txt' under RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1208 directory.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1209
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1210 The following four output files will be generated only by
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1211 prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1212
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1213 - 'sample_name.stat/sample_name_prsem.all_tr_features'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1214 It stores isofrom features for deriving and assigning pRSEM prior.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1215 The first line is a header and the rest is one isoform per line.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1216 The description for each column is:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1217
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1218 * trid: transcript ID from input annotation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1219
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1220 * geneid: gene ID from input anntation
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1221
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1222 * chrom: isoform's chromosome name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1223
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1224 * strand: isoform's strand name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1225
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1226 * start: isoform's end with the lowest genomic loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1227
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1228 * end: isoform's end with the highest genomic loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1229
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1230 * tss_mpp: average mappability of [TSS-500bp, TSS+500bp], where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1231 TSS is isoform's transcription start site, i.e. 5'-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1232
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1233 * body_mpp: average mappability of (TSS+500bp, TES-500bp), where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1234 TES is isoform's transcription end site, i.e. 3'-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1235
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1236 * tes_mpp: average mappability of [TES-500bp, TES+500bp]
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1237
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1238 * pme_count: isoform's fragment or read count from RSEM's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1239 posterior mean estimates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1240
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1241 * tss: isoform's TSS loci
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1242
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1243 * tss_pk: equal to 1 if isoform's [TSS-500bp, TSS+500bp] region
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1244 overlaps with a RNA Pol II peak; 0 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1245
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1246 * is_training: equal to 1 if isoform is in the training set where
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1247 Pol II prior is learned; 0 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1248
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1249 - 'sample_name.stat/sample_name_prsem.all_tr_prior'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1250 It stores prior parameters for every isoform. This file does not
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1251 have a header. Each line contains a prior parameter and an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1252 isoform's transcript ID delimited by " # ".
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1253
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1254 - 'sample_name.stat/sample_name_uniform_prior_1.isoforms.results'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1255 RSEM's posterior mean estimates on the isoform level with an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1256 initial pseudo-count of one for every isoform. It is in the same
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1257 format as the 'sample_name.isoforms.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1258
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1259 - 'sample_name.stat/sample_name_uniform_prior_1.genes.results'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1260 RSEM's posterior mean estimates on the gene level with an initial
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1261 pseudo-count of one for every isoform. It is in the same format as
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1262 the 'sample_name.genes.results'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1263
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1264 When learning prior from multiple external data sets in
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1265 prior-enhanced RSEM, two additional output files will be generated.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1266
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1267 - 'sample_name.stat/sample_name.pval_LL'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1268 It stores a p-value and a log-likelihood. The p-value indicates
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1269 whether the combination of multiple complementary data sets is
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1270 informative for RNA-seq quantification. The log-likelihood shows
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1271 how well pRSEM's Dirichlet-multinomial model fits the read counts
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1272 of partitioned training set isoforms.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1273
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1274 - 'sample_name.stat/sample_name.lgt_mdl.RData'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1275 It stores an R object named 'glmmdl', which is a logistic
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1276 regression model on the training set isoforms and multiple
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1277 external data sets.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1278
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1279 In addition, extra columns will be added to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1280 'sample_name.stat/all_tr_features'
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1281
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1282 * is_expr: equal to 1 if isoform has an abundance &gt;= 1 TPM and a
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1283 non-zero read count from RSEM's posterior mean estimates; 0
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1284 otherwise
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1285
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1286 * "$external_data_set_basename": log10 of external data's signal at
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1287 [TSS-500, TSS+500]. Signal is the number of reads aligned within
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1288 that interval and normalized to RPKM by read depth and interval
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1289 length. It will be set to -4 if no read aligned to that interval.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1290
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1291 There are multiple columns like this one, where each represents an
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1292 external data set.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1293
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1294 * prd_expr_prob: predicted probability from logistic regression
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1295 model on whether this isoform is expressed or not. A probability
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1296 higher than 0.5 is considered as expressed
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1297
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1298 * partition: group index, to which this isoforms is partitioned
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1299
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1300 * prior: prior parameter for this isoform
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1301
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1302 EXAMPLES
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1303 Assume the path to the bowtie executables is in the user's PATH
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1304 environment variable. Reference files are under '/ref' with name
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1305 'mouse_125'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1306
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1307 1) '/data/mmliver.fq', single-end reads with quality scores. Quality
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1308 scores are encoded as for 'GA pipeline version &gt;= 1.3'. We want to use 8
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1309 threads and generate a genome BAM file. In addition, we want to append
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1310 gene/transcript names to the result files:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1311
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1312 rsem-calculate-expression --phred64-quals \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1313 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1314 --append-names \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1315 --output-genome-bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1316 /data/mmliver.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1317 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1318 mmliver_single_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1319
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1320 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', stranded paired-end
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1321 reads with quality scores. Suppose the library is prepared using TruSeq
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1322 Stranded Kit, which means the first mate should map to the reverse
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1323 strand. Quality scores are in SANGER format. We want to use 8 threads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1324 and do not generate a genome BAM file:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1325
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1326 rsem-calculate-expression -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1327 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1328 --strandedness reverse \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1329 /data/mmliver_1.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1330 /data/mmliver_2.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1331 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1332 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1333
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1334 3) '/data/mmliver.fa', single-end reads without quality scores. We want
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1335 to use 8 threads:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1336
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1337 rsem-calculate-expression -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1338 --no-qualities \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1339 /data/mmliver.fa \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1340 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1341 mmliver_single_without_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1342
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1343 4) Data are the same as 1). This time we assume the bowtie executables
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1344 are under '/sw/bowtie'. We want to take a fragment length distribution
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1345 into consideration. We set the fragment length mean to 150 and the
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1346 standard deviation to 35. In addition to a BAM file, we also want to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1347 generate credibility intervals. We allow RSEM to use 1GB of memory for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1348 CI calculation:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1349
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1350 rsem-calculate-expression --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1351 --phred64-quals \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1352 --fragment-length-mean 150.0 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1353 --fragment-length-sd 35.0 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1354 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1355 --output-genome-bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1356 --calc-ci \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1357 --ci-memory 1024 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1358 /data/mmliver.fq \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1359 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1360 mmliver_single_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1361
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1362 5) '/data/mmliver_paired_end_quals.bam', BAM-formatted alignments for
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1363 paired-end reads with quality scores. We want to use 8 threads:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1364
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1365 rsem-calculate-expression --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1366 --alignments \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1367 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1368 /data/mmliver_paired_end_quals.bam \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1369 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1370 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1371
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1372 6) '/data/mmliver_1.fq.gz' and '/data/mmliver_2.fq.gz', paired-end reads
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1373 with quality scores and read files are compressed by gzip. We want to
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1374 use STAR to aligned reads and assume STAR executable is '/sw/STAR'.
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1375 Suppose we want to use 8 threads and do not generate a genome BAM file:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1376
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1377 rsem-calculate-expression --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1378 --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1379 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1380 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1381 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1382 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1383 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1384 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1385 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1386 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1387
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1388 7) In the above example, suppose we want to run prior-enhanced RSEM
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1389 instead. Assuming we want to learn priors from a ChIP-seq peak file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1390 '/data/mmlive.narrowPeak.gz':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1391
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1392 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1393 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1394 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1395 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1396 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1397 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1398 --chipseq-peak-file /data/mmliver.narrowPeak.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1399 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1400 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1401 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1402 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1403 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1404
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1405 8) Similar to the example in 7), suppose we want to use the partition
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1406 model 'pk_lm2nopk' (partitioning isoforms by Pol II TSS peak first and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1407 then partitioning 'no TSS peak' isoforms into two bins by a linear
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1408 regression model), and we want to partition isoforms by RNA Pol II's
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1409 ChIP-seq read files '/data/mmliver_PolIIRep1.fq.gz' and
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1410 '/data/mmliver_PolIIRep2.fq.gz', and the control ChIP-seq read files
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1411 '/data/mmliver_ChIPseqCtrl.fq.gz'. Also, assuming Bowtie's executables
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1412 are under '/sw/bowtie/':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1413
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1414 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1415 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1416 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1417 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1418 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1419 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1420 --chipseq-target-read-files /data/mmliver_PolIIRep1.fq.gz,/data/mmliver_PolIIRep2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1421 --chipseq-control-read-files /data/mmliver_ChIPseqCtrl.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1422 --partition-model pk_lm2nopk \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1423 --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1424 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1425 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1426 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1427 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1428 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
artbio
parents:
diff changeset
1429
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1430 9) Similar to the example in 8), suppose we want to derive prior from
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1431 four histone modification ChIP-seq read data sets:
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1432 '/data/H3K27Ac.fastq.gz', '/data/H3K4me1.fastq.gz',
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1433 '/data/H3K4me2.fastq.gz', and '/data/H3K4me3.fastq.gz'. Also, assuming
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1434 Bowtie's executables are under '/sw/bowtie/':
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1435
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1436 rsem-calculate-expression --star \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1437 --star-path /sw/STAR \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1438 --gzipped-read-file \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1439 --paired-end \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1440 --calc-pme \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1441 --run-pRSEM \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1442 --partition-model cmb_lgt \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1443 --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1444 --bowtie-path /sw/bowtie \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1445 -p 8 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1446 /data/mmliver_1.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1447 /data/mmliver_2.fq.gz \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1448 /ref/mouse_125 \
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1449 mmliver_paired_end_quals
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1450
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1451 </help>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1452 <citations>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1453 <citation type="doi">10.1186/1471-2105-12-323</citation>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1454 </citations>
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1455
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1456 </tool>