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annotate rsem-bwt2.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="rsembowtie2" name="RSEM-Bowtie2" version="@WRAPPER_VERSION@">
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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2 <description></description>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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3 <macros>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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4 <import>macros.xml</import>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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5 </macros>
11
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" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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7 <stdio>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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8 <exit_code range="1:" level="warning" description="Tool exception" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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9 </stdio>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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10 <command detect_errors="exit_code"><![CDATA[
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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11 #if $job.select_job == "index":
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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12 echo ${job.reference_name} " " | tee $reference_file &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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13 mkdir $reference_file.files_path &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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14 rsem-prepare-reference
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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15 #if $job.polya.polya_use == 'add':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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16 #if $job.polya.polya_length:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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17 --polyA-length $job.polya.polya_length
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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18 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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19 #elif $job.polya.polya_use == 'subset':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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20 --no-polyA-subset $job.polya.no_polya_subset
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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21 #if $job.polya.polya_length:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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22 --polyA-length $job.polya.polya_length
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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23 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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24 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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25 $job.ntog
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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28 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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29 --bowtie2
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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30 #if $job.self_reference.ref_type == 'transcripts':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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31 $job.self_reference.reference_fasta_file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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32 #else:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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33 --gtf $job.self_reference.gtf
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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34 $job.self_reference.reference_fasta_file
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35 #end if
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36 ${reference_file.files_path}/${job.reference_name}
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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37 > ${reference_file.files_path}/${job.reference_name}.log
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38 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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39
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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40 #if $job.select_job == "index" and $run_rsem.select == "Yes":
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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41 &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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42 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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43
10
6aba6cca3fab planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
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44 #if $run_rsem.select == "Yes" and $run_rsem.input.format == 'fastq':
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":
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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47 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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48 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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49 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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50 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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":
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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53 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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54 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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 $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'):
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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57 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
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58 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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59 #end if
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60 #end if
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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80 #end if
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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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
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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86 #end if
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87 #end if
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88 ## Calculate 95% credibility intervals and posterior mean estimates.
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89 #if $run_rsem.rsem_options.useci.ci == 'yes':
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90 --calc-ci
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91 #if $run_rsem.rsem_options.useci.cimem:
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92 --ci-memory $run_rsem.rsem_options.useci.cimem
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93 #end if
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94 #end if
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95 #end if
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96 --num-threads \${GALAXY_SLOTS:-4}
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97 --bowtie2
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98 #if $run_rsem.input.format == 'fasta' and $run_rsem.input.bowtie2_options.fullparams == 'fullset':
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99 ## Bowtie params
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100 #if $run_rsem.input.bowtie2_options.bowtie2_mismatch_rate:
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101 --bowtie2-mismatch-rate $run_rsem.input.bowtie2_options.bowtie2_mismatch_rate
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102 #end if
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103 #if $run_rsem.input.bowtie2_options.bowtie2_k:
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104 --bowtie2-k $run_rsem.input.bowtie2_options.bowtie2_k
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105 #end if
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106 #if $run_rsem.input.bowtie2_options.bowtie2_sensitivity_level:
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107 --bowtie2-sensitivity-level $run_rsem.input.bowtie2_options.bowtie2_sensitivity_level
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108 #end if
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109 #end if
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110 ## Outputs
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111 #if $run_rsem.rsem_outputs.result_bams == 'none':
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112 --no-bam-output
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113 #elif $run_rsem.rsem_outputs.result_bams == 'default':
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114 --sort-bam-by-coordinate
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115 #else
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116 --sort-bam-by-coordinate
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117 --output-genome-bam
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118 $run_rsem.rsem_outputs.sampling_for_bam
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119 #end if
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120 ## Input data
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121 #if $run_rsem.input.format=="fastq"
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122 $run_rsem.input.fastq_select
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123 #if $run_rsem.input.fastq.matepair=="single":
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124 uncomp_single.fastq
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125 #elif $run_rsem.input.fastq.matepair=="paired":
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126 --paired-end
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127 uncomp_pair1.fastq
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128 uncomp_pair2.fastq
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129 #end if
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130 #elif $run_rsem.input.format=="fasta"
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131 --no-qualities
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132 #if $run_rsem.input.fasta.matepair=="single":
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133 $run_rsem.input.fasta.singlefasta
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134 #elif $run_rsem.input.fasta.matepair=="paired":
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135 --paired-end
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136 $run_rsem.input.fasta.fasta1
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137 $run_rsem.input.fasta.fasta2
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138 #end if
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139 #end if
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140 ## RSEM reference
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141 #if $run_rsem.reference.refSrc == 'history':
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142 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
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143 #elif $run_rsem.reference.refSrc == 'self':
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144 ${reference_file.files_path}/${job.reference_name}
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145 #end if
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146 ## sample_name: use a hard coded name so we can pull out galaxy outputs
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147 rsem_output
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148 ## direct output into logfile
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149 > $log
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150 #end if
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151 ]]></command>
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152
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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153 <inputs>
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154 <conditional name="job">
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155 <param name="select_job" type="select" label="rsem reference">
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156 <option value="index">Build rsem reference</option>
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157 <option value="no-index" selected="true">rsem reference available from history</option>
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158 </param>
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159 <when value="index">
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160 <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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161 <param name="ref_type" type="select" label="Reference source">
5
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162 <option value="transcripts">transcript fasta</option>
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163 <option value="genomic">reference genome and gtf</option>
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164 </param>
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165 <when value="transcripts">
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166 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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167 help="The files should contain the sequences of transcripts."/>
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168 </when>
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169 <when value="genomic">
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170 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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171 help="The file should contain the sequence of an entire genome."/>
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172 <param name="gtf" type="data" format="gtf" label="gtf"
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173 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
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174 </when>
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175 </conditional>
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176 <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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177 <help>
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178 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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179 The map can be obtained from the UCSC table browser
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180 group: Genes and Gene Prediction Tracks
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181 table: knownIsoforms
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182 Without a map:
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183 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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184 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
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185 </help>
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186 </param>
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187 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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188 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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189 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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190 </param>
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191 <conditional name="polya">
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192 <param name="polya_use" type="select" label="PolyA ">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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193 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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194 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
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195 <option value="none">Do not add poly(A) tails to any transcripts</option>
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196 </param>
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197 <when value="add">
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198 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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199 <validator type="in_range" message="must be positive " min="1"/>
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200 </param>
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201 </when>
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202 <when value="subset">
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203 <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."/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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204 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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205 <validator type="in_range" message="must be positive " min="1"/>
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206 </param>
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207 </when>
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208 <when value="none"/>
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209 </conditional>
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210 <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."/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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211 </when>
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212 <when value="no-index">
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213 </when>
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214 </conditional>
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215
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216 <conditional name="run_rsem">
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217 <param name="select" type="select" label="calculate expression with rsem">
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218 <option value="No">Just build rsem reference for latter rsem profiling</option>
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219 <option value="Yes" selected="true">profile expression with rsem</option>
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220 </param>
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221 <when value="Yes">
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222 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
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223 <conditional name="reference">
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224 <param name="refSrc" type="select" label="RSEM Reference Source">
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225 <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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226 <option value="self">RSEM Reference prepared with this tool</option>
5
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227 </param>
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228 <when value="history">
9
cf60c3338279 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 62e8088d5f73cbb9b2f93e23a74636c77a06b492
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229 <param name="rsem_ref" type="data" format="rsem_bt2_ref" label="RSEM reference" />
5
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230 </when>
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231 <when value="self">
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232 </when>
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233 </conditional>
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234 <conditional name="input">
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235 <param name="format" type="select" label="RSEM Input file type">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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236 <option value="fastq">FASTQ</option>
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237 <option value="fasta">FASTA</option>
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238 </param>
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239 <when value="fastq">
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240 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
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241 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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242 <option value="--solexa-quals">solexa qualities</option>
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243 <option value="--phred64-quals">phred64 qualities</option>
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244 </param>
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245 <conditional name="fastq">
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246 <param name="matepair" type="select" label="Library type">
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247 <option value="single">Single End Reads</option>
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248 <option value="paired">Paired End Reads</option>
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249 </param>
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250 <when value="single">
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251 <param name="singlefastq" type="data" format="fastq,fastq.gz" label="FASTQ file" />
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252 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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253 <when value="paired">
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254 <param name="fastq1" type="data" format="fastq,fastq.gz" label="Read 1 fastq file" />
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255 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Read 2 fastq file" />
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256 </when>
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257 </conditional>
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258 <expand macro="bowtie2_options"/>
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259 </when>
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260 <when value="fasta">
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261 <conditional name="fasta">
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262 <param name="matepair" type="select" label="Library Type">
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263 <option value="single">Single End Reads</option>
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264 <option value="paired">Paired End Reads</option>
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265 </param>
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266 <when value="single">
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267 <param name="singlefasta" type="data" format="fasta" label="fasta file" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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268 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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269 <when value="paired">
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artbio
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270 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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271 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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272 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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273 </conditional>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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274 <expand macro="bowtie2_options"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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275 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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276 </conditional>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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277 <expand macro="rsem_options"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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278 <conditional name="rsem_outputs">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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279 <param name="result_bams" type="select" label="Create bam results files"
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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280 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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281 <option value="none">No BAM results files</option>
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artbio
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282 <option value="default" selected="true">Transcript BAM results file</option>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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283 <option value="both">Transcript and genome BAM results files</option>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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284 </param>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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285 <when value="none"/>
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286 <when value="default">
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artbio
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287 <expand macro="sampling_for_bam"/>
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288 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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289 <when value="both">
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artbio
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diff changeset
290 <expand macro="sampling_for_bam"/>
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291 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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292 </conditional>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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293 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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294 <when value="No">
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295 </when>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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296 </conditional>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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297 </inputs>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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298
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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299 <outputs>
9
cf60c3338279 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 62e8088d5f73cbb9b2f93e23a74636c77a06b492
artbio
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diff changeset
300 <data format="rsem_bt2_ref" name="reference_file" label="RSEM ${job.reference_name} reference">
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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301 <filter>job['select_job'] == "index"</filter>
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302 </data>
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artbio
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diff changeset
303 <data format="tabular" name="gene_abundances" label="${run_rsem.sample}.gene_abundances" from_work_dir="rsem_output.genes.results">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
304 <filter>run_rsem['select'] == "Yes"</filter>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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305 </data>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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306 <data format="tabular" name="isoform_abundances" label="${run_rsem.sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
307 <filter>run_rsem['select'] == "Yes"</filter>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
308 </data>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
309 <data format="bam" name="transcript_sorted_bam" label="${run_rsem.sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
310 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] != "none"</filter>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
311 </data>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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312 <data format="bam" name="genome_sorted_bam" label="${run_rsem.sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
313 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] == "both"</filter>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
314 </data>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
315 <data format="txt" name="log" label="${run_rsem.sample}.rsem_log">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
316 <filter>run_rsem['select'] == "Yes"</filter>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
317 </data>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
318 </outputs>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
319
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
320 <tests>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
321 <test>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
322 <param name="select_job" value="index"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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323 <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
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diff changeset
324 <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
325 <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
326 <param name="reference_name" value="ebola_genome"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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327 <param name="select" value="Yes"/>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
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diff changeset
328 <param name="sample" value="ebola_RNAseq"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
329 <param name="refSrc" value="self"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
330 <param name="format" value="fastq"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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331 <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
332 <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
333 <param name="result_bams" value="none"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
334 <output name="reference_file">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
335 <assert_contents>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
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diff changeset
336 <has_text text="ebola_genome" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
337 </assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
338 </output>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
339 <output name="gene_abundances" value="refgen_gene_abundances.bt2.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
340 <output name="isoform_abundances" value="refgen_isoform_abundances.bt2.tab" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
341 <output name="log">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
342 <assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
343 <has_text text="Expression Results are written" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
344 </assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
345 </output>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
346 </test>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
347 <test>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
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diff changeset
348 <!-- test paired end on ebola genome -->
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
349 <param name="select_job" value="index"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
350 <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
351 <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
352 <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
353 <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
354 <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
355 <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
356 <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
357 <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
358 <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
359 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
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="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
361 <param name="result_bams" value="both"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
362 <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
363 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
364 <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
365 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
366 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
367 <output name="gene_abundances" value="paired_refgen_gene_abundances.bt2.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
368 <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt2.tab" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
369 <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt2.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
370 <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt2.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
371 <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
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 <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
374 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
375 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
376 </test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
377 <test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
378 <!-- test paired end on ebola transcripts -->
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
379 <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
380 <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
381 <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
382 <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="gtf"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
383 <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
384 <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
385 <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
386 <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
387 <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
388 <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
389 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
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="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
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="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
392 <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
393 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
394 <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
395 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
396 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
397 <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt2.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
398 <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt2.tab" />
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="transcript_sorted_bam" value="paired_reftrans_transcripts.bt2.bam" ftype="bam" lines_diff="2" />
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
400 <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
401 <assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
402 <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
403 </assert_contents>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
404 </output>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
405 </test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
406 <test>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
407 <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
408 <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
409 <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
410 <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
411 <param name="reference_name" value="ebola"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
412 <param name="select" value="Yes"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
413 <param name="sample" value="rsem_sample"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
414 <param name="refSrc" value="self"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
415 <param name="format" value="fastq"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
416 <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
417 <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
418 <param name="result_bams" value="none"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
419 <output name="reference_file">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
420 <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
421 <has_text text="ebola" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
422 </assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
423 </output>
11
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
424 <output name="gene_abundances" value="single_refgen_gene_abundances.bt2.tab"/>
c86ed39b72eb "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
artbio
parents: 10
diff changeset
425 <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt2.tab" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
426 <output name="log">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
427 <assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
428 <has_text text="Expression Results are written" />
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
429 </assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
430 </output>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
431 </test>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
432 <test>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
433 <param name="select_job" value="index"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
434 <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
435 <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
436 <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
437 <param name="reference_name" value="alone"/>
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
438 <param name="select" value="No"/>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
439 <output name="reference_file">
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
440 <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
441 <has_text text="alone" />
5
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
442 </assert_contents>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
443 </output>
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444 </test>
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445 </tests>
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446
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447 <help>
6
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448 .. class:: infomark
5
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449
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450 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
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451
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452 NAME
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453 rsem-prepare-reference
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454
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455 SYNOPSIS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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456 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
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457
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458 DESCRIPTION
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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459 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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460 This program is used in conjunction with the 'rsem-calculate-expression' program.
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461
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462 INPUTS
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463 A fasta file of transcripts
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464 or
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465 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
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466
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467 ---
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468
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469 NAME
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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470 rsem-calculate-expression - Estimate gene and isoform expression from
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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471 RNA-Seq data.
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472
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473 SYNOPSIS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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474 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
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475 rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
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476 rsem-calculate-expression [options] --alignments [--paired-end] input reference_name sample_name
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477
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478 ARGUMENTS
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479 upstream_read_files(s)
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480 Comma-separated list of files containing single-end reads or
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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481 upstream reads for paired-end data. By default, these files are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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482 assumed to be in FASTQ format. If the --no-qualities option is
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483 specified, then FASTA format is expected.
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484
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485 downstream_read_file(s)
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486 Comma-separated list of files containing downstream reads which are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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487 paired with the upstream reads. By default, these files are assumed
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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488 to be in FASTQ format. If the --no-qualities option is specified,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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489 then FASTA format is expected.
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490
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491 input
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492 SAM/BAM/CRAM formatted input file. If "-" is specified for the
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493 filename, the input is instead assumed to come from standard input.
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494 RSEM requires all alignments of the same read group together. For
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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495 paired-end reads, RSEM also requires the two mates of any alignment
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496 be adjacent. In addition, RSEM does not allow the SEQ and QUAL
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497 fields to be empty. See Description section for how to make input
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498 file obey RSEM's requirements.
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499
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500 reference_name
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501 The name of the reference used. The user must have run
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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502 'rsem-prepare-reference' with this reference_name before running
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503 this program.
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504
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505 sample_name
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506 The name of the sample analyzed. All output files are prefixed by
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507 this name (e.g., sample_name.genes.results)
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508
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509 BASIC OPTIONS
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510 --paired-end
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511 Input reads are paired-end reads. (Default: off)
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512
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513 --no-qualities
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514 Input reads do not contain quality scores. (Default: off)
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515
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516 --strandedness &lt;none|forward|reverse&gt;
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517 This option defines the strandedness of the RNA-Seq reads. It
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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518 recognizes three values: 'none', 'forward', and 'reverse'. 'none'
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519 refers to non-strand-specific protocols. 'forward' means all
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520 (upstream) reads are derived from the forward strand. 'reverse'
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521 means all (upstream) reads are derived from the reverse strand. If
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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522 'forward'/'reverse' is set, the '--norc'/'--nofw' Bowtie/Bowtie 2
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523 option will also be enabled to avoid aligning reads to the opposite
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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524 strand. For Illumina TruSeq Stranded protocols, please use
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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525 'reverse'. (Default: 'none')
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526
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527 -p/--num-threads &lt;int&gt;
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528 Number of threads to use. Both Bowtie/Bowtie2, expression estimation
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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529 and 'samtools sort' will use this many threads. (Default: 1)
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530
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531 --alignments
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532 Input file contains alignments in SAM/BAM/CRAM format. The exact
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533 file format will be determined automatically. (Default: off)
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534
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535 --fai &lt;file&gt;
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536 If the header section of input alignment file does not contain
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diff changeset
537 reference sequence information, this option should be turned on.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
538 &lt;file&gt; is a FAI format file containing each reference sequence's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
539 name and length. Please refer to the SAM official website for the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
540 details of FAI format. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
541
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
542 --bowtie2
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
543 Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
544 does not handle indel, local and discordant alignments, the Bowtie2
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
545 parameters are set in a way to avoid those alignments. In
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
546 particular, we use options '--sensitive --dpad 0 --gbar 99999999
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
547 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. The last parameter
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
548 of '--score-min', '-0.1', is the negative of maximum mismatch rate.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
549 This rate can be set by option '--bowtie2-mismatch-rate'. If reads
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
550 are paired-end, we additionally use options '--no-mixed' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
551 '--no-discordant'. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
552
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
553 --star
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
554 Use STAR to align reads. Alignment parameters are from ENCODE3's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
555 STAR-RSEM pipeline. To save computational time and memory resources,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
556 STAR's Output BAM file is unsorted. It is stored in RSEM's temporary
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
557 directory with name as 'sample_name.bam'. Each STAR job will have
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
558 its own private copy of the genome in memory. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
559
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
560 --append-names
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
561 If gene_name/transcript_name is available, append it to the end of
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
562 gene_id/transcript_id (separated by '_') in files
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
563 'sample_name.isoforms.results' and 'sample_name.genes.results'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
564 (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
565
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
566 --seed &lt;uint32&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
567 Set the seed for the random number generators used in calculating
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
568 posterior mean estimates and credibility intervals. The seed must be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
569 a non-negative 32 bit integer. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
570
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
571 --single-cell-prior
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
572 By default, RSEM uses Dirichlet(1) as the prior to calculate
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
573 posterior mean estimates and credibility intervals. However, much
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
574 less genes are expressed in single cell RNA-Seq data. Thus, if you
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
575 want to compute posterior mean estimates and/or credibility
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
576 intervals and you have single-cell RNA-Seq data, you are recommended
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
577 to turn on this option. Then RSEM will use Dirichlet(0.1) as the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
578 prior which encourage the sparsity of the expression levels.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
579 (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
580
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
581 --calc-pme
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
582 Run RSEM's collapsed Gibbs sampler to calculate posterior mean
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
583 estimates. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
584
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
585 --calc-ci
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
586 Calculate 95% credibility intervals and posterior mean estimates.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
587 The credibility level can be changed by setting
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
588 '--ci-credibility-level'. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
589
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
590 -q/--quiet
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
591 Suppress the output of logging information. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
592
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
593 -h/--help
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
594 Show help information.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
595
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
596 --version
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
597 Show version information.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
598
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
599 OUTPUT OPTIONS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
600 --sort-bam-by-read-name
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
601 Sort BAM file aligned under transcript coordidate by read name.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
602 Setting this option on will produce deterministic maximum likelihood
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
603 estimations from independent runs. Note that sorting will take long
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
604 time and lots of memory. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
605
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
606 --no-bam-output
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
607 Do not output any BAM file. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
608
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
609 --sampling-for-bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
610 When RSEM generates a BAM file, instead of outputting all alignments
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
611 a read has with their posterior probabilities, one alignment is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
612 sampled according to the posterior probabilities. The sampling
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
613 procedure includes the alignment to the "noise" transcript, which
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
614 does not appear in the BAM file. Only the sampled alignment has a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
615 weight of 1. All other alignments have weight 0. If the "noise"
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
616 transcript is sampled, all alignments appeared in the BAM file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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617 should have weight 0. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
618
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
619 --output-genome-bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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620 Generate a BAM file, 'sample_name.genome.bam', with alignments
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
621 mapped to genomic coordinates and annotated with their posterior
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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622 probabilities. In addition, RSEM will call samtools (included in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
623 RSEM package) to sort and index the bam file.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
624 'sample_name.genome.sorted.bam' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
625 'sample_name.genome.sorted.bam.bai' will be generated. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
626 off)
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627
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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628 --sort-bam-by-coordinate
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
629 Sort RSEM generated transcript and genome BAM files by coordinates
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
630 and build associated indices. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
631
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
632 --sort-bam-memory-per-thread &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
633 Set the maximum memory per thread that can be used by 'samtools
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
634 sort'. &lt;string&gt; represents the memory and accepts suffices 'K/M/G'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
635 RSEM will pass &lt;string&gt; to the '-m' option of 'samtools sort'. Note
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
636 that the default used here is different from the default used by
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
637 samtools. (Default: 1G)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
638
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
639 ALIGNER OPTIONS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
640 --seed-length &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
641 Seed length used by the read aligner. Providing the correct value is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
642 important for RSEM. If RSEM runs Bowtie, it uses this value for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
643 Bowtie's seed length parameter. Any read with its or at least one of
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
644 its mates' (for paired-end reads) length less than this value will
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
645 be ignored. If the references are not added poly(A) tails, the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
646 minimum allowed value is 5, otherwise, the minimum allowed value is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
647 25. Note that this script will only check if the value &gt;= 5 and give
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
648 a warning message if the value &lt; 25 but &gt;= 5. (Default: 25)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
649
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
650 --phred33-quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
651 Input quality scores are encoded as Phred+33. (Default: on)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
652
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
653 --phred64-quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
654 Input quality scores are encoded as Phred+64 (default for GA
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
655 Pipeline ver. &gt;= 1.3). (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
656
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
657 --solexa-quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
658 Input quality scores are solexa encoded (from GA Pipeline ver. &lt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
659 1.3). (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
660
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
661 --bowtie-path &lt;path&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
662 The path to the Bowtie executables. (Default: the path to the Bowtie
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
663 executables is assumed to be in the user's PATH environment
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
664 variable)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
665
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
666 --bowtie-n &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
667 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
668 Default: 2)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
669
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
670 --bowtie-e &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
671 (Bowtie parameter) max sum of mismatch quality scores across the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
672 alignment. (Default: 99999999)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
673
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
674 --bowtie-m &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
675 (Bowtie parameter) suppress all alignments for a read if &gt; &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
676 valid alignments exist. (Default: 200)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
677
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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678 --bowtie-chunkmbs &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
679 (Bowtie parameter) memory allocated for best first alignment
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
680 calculation (Default: 0 - use Bowtie's default)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
681
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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682 --bowtie2-path &lt;path&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
683 (Bowtie 2 parameter) The path to the Bowtie 2 executables. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
684 the path to the Bowtie 2 executables is assumed to be in the user's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
685 PATH environment variable)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
686
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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687 --bowtie2-mismatch-rate &lt;double&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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688 (Bowtie 2 parameter) The maximum mismatch rate allowed. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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689 0.1)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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690
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691 --bowtie2-k &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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692 (Bowtie 2 parameter) Find up to &lt;int&gt; alignments per read. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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693 200)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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694
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695 --bowtie2-sensitivity-level &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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696 (Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
697 mode. This option controls how hard Bowtie 2 tries to find
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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698 alignments. &lt;string&gt; must be one of "very_fast", "fast", "sensitive"
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
699 and "very_sensitive". The four candidates correspond to Bowtie 2's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
700 "--very-fast", "--fast", "--sensitive" and "--very-sensitive"
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
701 options. (Default: "sensitive" - use Bowtie 2's default)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
702
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
703 --star-path &lt;path&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
704 The path to STAR's executable. (Default: the path to STAR executable
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
705 is assumed to be in user's PATH environment variable)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
706
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
707 --star-gzipped-read-file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
708 (STAR parameter) Input read file(s) is compressed by gzip. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
709 off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
710
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
711 --star-bzipped-read-file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
712 (STAR parameter) Input read file(s) is compressed by bzip2.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
713 (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
714
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
715 --star-output-genome-bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
716 (STAR parameter) Save the BAM file from STAR alignment under genomic
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
717 coordinate to 'sample_name.STAR.genome.bam'. This file is NOT sorted
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
718 by genomic coordinate. In this file, according to STAR's manual,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
719 'paired ends of an alignment are always adjacent, and multiple
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
720 alignments of a read are adjacent as well'. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
721
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
722 ADVANCED OPTIONS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
723 --tag &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
724 The name of the optional field used in the SAM input for identifying
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
725 a read with too many valid alignments. The field should have the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
726 format &lt;tagName&gt;:i:&lt;value&gt;, where a &lt;value&gt; bigger than 0 indicates
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
727 a read with too many alignments. (Default: "")
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
728
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
729 --fragment-length-min &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
730 Minimum read/insert length allowed. This is also the value for the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
731 Bowtie/Bowtie2 -I option. (Default: 1)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
732
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
733 --fragment-length-max &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
734 Maximum read/insert length allowed. This is also the value for the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
735 Bowtie/Bowtie 2 -X option. (Default: 1000)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
736
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
737 --fragment-length-mean &lt;double&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
738 (single-end data only) The mean of the fragment length distribution,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
739 which is assumed to be a Gaussian. (Default: -1, which disables use
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
740 of the fragment length distribution)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
741
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
742 --fragment-length-sd &lt;double&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
743 (single-end data only) The standard deviation of the fragment length
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
744 distribution, which is assumed to be a Gaussian. (Default: 0, which
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
745 assumes that all fragments are of the same length, given by the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
746 rounded value of --fragment-length-mean)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
747
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
748 --estimate-rspd
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
749 Set this option if you want to estimate the read start position
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
750 distribution (RSPD) from data. Otherwise, RSEM will use a uniform
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
751 RSPD. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
752
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
753 --num-rspd-bins &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
754 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
755 specified. Use of the default setting is recommended. (Default: 20)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
756
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
757 --gibbs-burnin &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
758 The number of burn-in rounds for RSEM's Gibbs sampler. Each round
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
759 passes over the entire data set once. If RSEM can use multiple
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
760 threads, multiple Gibbs samplers will start at the same time and all
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
761 samplers share the same burn-in number. (Default: 200)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
762
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
763 --gibbs-number-of-samples &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
764 The total number of count vectors RSEM will collect from its Gibbs
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
765 samplers. (Default: 1000)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
766
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
767 --gibbs-sampling-gap &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
768 The number of rounds between two succinct count vectors RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
769 collects. If the count vector after round N is collected, the count
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
770 vector after round N + &lt;int&gt; will also be collected. (Default: 1)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
771
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
772 --ci-credibility-level &lt;double&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
773 The credibility level for credibility intervals. (Default: 0.95)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
774
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
775 --ci-memory &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
776 Maximum size (in memory, MB) of the auxiliary buffer used for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
777 computing credibility intervals (CI). (Default: 1024)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
778
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
779 --ci-number-of-samples-per-count-vector &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
780 The number of read generating probability vectors sampled per
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
781 sampled count vector. The crebility intervals are calculated by
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
782 first sampling P(C | D) and then sampling P(Theta | C) for each
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
783 sampled count vector. This option controls how many Theta vectors
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
784 are sampled per sampled count vector. (Default: 50)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
785
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
786 --keep-intermediate-files
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
787 Keep temporary files generated by RSEM. RSEM creates a temporary
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
788 directory, 'sample_name.temp', into which it puts all intermediate
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
789 output files. If this directory already exists, RSEM overwrites all
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
790 files generated by previous RSEM runs inside of it. By default,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
791 after RSEM finishes, the temporary directory is deleted. Set this
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
792 option to prevent the deletion of this directory and the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
793 intermediate files inside of it. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
794
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
795 --temporary-folder &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
796 Set where to put the temporary files generated by RSEM. If the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
797 folder specified does not exist, RSEM will try to create it.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
798 (Default: sample_name.temp)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
799
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
800 --time
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
801 Output time consumed by each step of RSEM to 'sample_name.time'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
802 (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
803
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
804 PRIOR-ENHANCED RSEM OPTIONS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
805 --run-pRSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
806 Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
807 isoform's initial pseudo-count for RSEM's Gibbs sampling, will be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
808 learned from input RNA-seq data and an external data set. When pRSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
809 needs and only needs ChIP-seq peak information to partition isoforms
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
810 (e.g. in pRSEM's default partition model), either ChIP-seq peak file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
811 (with the '--chipseq-peak-file' option) or ChIP-seq FASTQ files for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
812 target and input and the path for Bowtie executables are required
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
813 (with the '--chipseq-target-read-files &lt;string&gt;',
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
814 '--chipseq-control-read-files &lt;string&gt;', and '--bowtie-path &lt;path&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
815 options), otherwise, ChIP-seq FASTQ files for target and control and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
816 the path to Bowtie executables are required. (Default: off)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
817
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
818 --chipseq-peak-file &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
819 Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
820 BED6+4, format. This file is used when running prior-enhanced RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
821 in the default two-partition model. It partitions isoforms by
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
822 whether they have ChIP-seq overlapping with their transcription
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
823 start site region or not. Each partition will have its own prior
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
824 parameter learned from a training set. This file can be either
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
825 gzipped or ungzipped. (Default: "")
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
826
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
827 --chipseq-target-read-files &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
828 Comma-separated full path of FASTQ read file(s) for ChIP-seq target.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
829 This option is used when running prior-enhanced RSEM. It provides
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
830 information to calculate ChIP-seq peaks and signals. The file(s) can
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
831 be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
832 options '--bowtie-path &lt;path&gt;' and '--chipseq-control-read-files
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
833 &lt;string&gt;' must be defined when this option is specified. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
834 "")
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
835
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
836 --chipseq-control-read-files &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
837 Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
838 This option is used when running prior-enhanced RSEM. It provides
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
839 information to call ChIP-seq peaks. The file(s) can be either
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
840 ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
841 '--bowtie-path &lt;path&gt;' and '--chipseq-target-read-files &lt;string&gt;'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
842 must be defined when this option is specified. (Default: "")
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
843
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
844 --chipseq-read-files-multi-targets &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
845 Comma-separated full path of FASTQ read files for multiple ChIP-seq
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
846 targets. This option is used when running prior-enhanced RSEM, where
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
847 prior is learned from multiple complementary data sets. It provides
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
848 information to calculate ChIP-seq signals. All files can be either
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
849 ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
850 option is specified, the option '--bowtie-path &lt;path&gt;' must be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
851 defined and the option '--partition-model &lt;string&gt;' will be set to
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
852 'cmb_lgt' automatically. (Default: "")
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
853
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
854 --chipseq-bed-files-multi-targets &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
855 Comma-separated full path of BED files for multiple ChIP-seq
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
856 targets. This option is used when running prior-enhanced RSEM, where
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
857 prior is learned from multiple complementary data sets. It provides
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
858 information of ChIP-seq signals and must have at least the first six
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
859 BED columns. All files can be either ungzipped or gzipped with a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
860 suffix '.gz' or '.gzip'. When this option is specified, the option
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
861 '--partition-model &lt;string&gt;' will be set to 'cmb_lgt' automatically.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
862 (Default: "")
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diff changeset
863
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
864 --cap-stacked-chipseq-reads
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
865 Keep a maximum number of ChIP-seq reads that aligned to the same
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
866 genomic interval. This option is used when running prior-enhanced
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
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diff changeset
867 RSEM, where prior is learned from multiple complementary data sets.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
868 This option is only in use when either
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
869 '--chipseq-read-files-multi-targets &lt;string&gt;' or
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
870 '--chipseq-bed-files-multi-targets &lt;string&gt;' is specified. (Default:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
871 off)
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diff changeset
872
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
873 --n-max-stacked-chipseq-reads &lt;int&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
874 The maximum number of stacked ChIP-seq reads to keep. This option is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
875 used when running prior-enhanced RSEM, where prior is learned from
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
876 multiple complementary data sets. This option is only in use when
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
877 the option '--cap-stacked-chipseq-reads' is set. (Default: 5)
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
878
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diff changeset
879 --partition-model &lt;string&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
880 A keyword to specify the partition model used by prior-enhanced
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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881 RSEM. It must be one of the following keywords:
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diff changeset
882
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diff changeset
883 - pk
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
884 Partitioned by whether an isoform has a ChIP-seq peak overlapping
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
885 with its transcription start site (TSS) region. The TSS region is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
886 defined as [TSS-500bp, TSS+500bp]. For simplicity, we refer this
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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887 type of peak as 'TSS peak' when explaining other keywords.
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diff changeset
888
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889 - pk_lgtnopk
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
890 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
891 peak' set, a logistic model is employed to further classify them
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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892 into two partitions.
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893
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894 - lm3, lm4, lm5, or lm6
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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895 Based on their ChIP-seq signals, isoforms are classified into 3,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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896 4, 5, or 6 partitions by a linear regression model.
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diff changeset
897
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898 - nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
899 First partitioned by TSS peak. Then, for isoforms in the 'with TSS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
900 peak' set, a linear regression model is employed to further
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
901 classify them into 2, 3, 4, or 5 partitions.
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diff changeset
902
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parents:
diff changeset
903 - pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
904 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
905 peak' set, a linear regression model is employed to further
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
906 classify them into 2, 3, 4, or 5 partitions.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
907
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
908 - cmb_lgt
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
909 Using a logistic regression to combine TSS signals from multiple
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
910 complementary data sets and partition training set isoform into
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
911 'expressed' and 'not expressed'. This partition model is only in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
912 use when either '--chipseq-read-files-multi-targets &lt;string&gt;' or
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
913 '--chipseq-bed-files-multi-targets &lt;string&gt; is specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
914
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parents:
diff changeset
915 Parameters for all the above models are learned from a training set.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
916 For detailed explanations, please see prior-enhanced RSEM's paper.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
917 (Default: 'pk')
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parents:
diff changeset
918
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parents:
diff changeset
919 DEPRECATED OPTIONS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
920 The options in this section are deprecated. They are here only for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
921 compatibility reasons and may be removed in future releases.
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parents:
diff changeset
922
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parents:
diff changeset
923 --sam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
924 Inputs are alignments in SAM format. (Default: off)
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parents:
diff changeset
925
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parents:
diff changeset
926 --bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
927 Inputs are alignments in BAM format. (Default: off)
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parents:
diff changeset
928
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parents:
diff changeset
929 --strand-specific
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
930 Equivalent to '--strandedness forward'. (Default: off)
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parents:
diff changeset
931
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diff changeset
932 --forward-prob &lt;double&gt;
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
933 Probability of generating a read from the forward strand of a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
934 transcript. Set to 1 for a strand-specific protocol where all
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
935 (upstream) reads are derived from the forward strand, 0 for a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
936 strand-specific protocol where all (upstream) read are derived from
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parents:
diff changeset
937 the reverse strand, or 0.5 for a non-strand-specific protocol.
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938 (Default: off)
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diff changeset
939
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940 DESCRIPTION
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diff changeset
941 In its default mode, this program aligns input reads against a reference
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
942 transcriptome with Bowtie and calculates expression values using the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
943 alignments. RSEM assumes the data are single-end reads with quality
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
944 scores, unless the '--paired-end' or '--no-qualities' options are
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parents:
diff changeset
945 specified. Alternatively, users can use STAR to align reads using the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
946 '--star' option. RSEM has provided options in 'rsem-prepare-reference'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
947 to prepare STAR's genome indices. Users may use an alternative aligner
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
948 by specifying '--alignments', and providing an alignment file in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
949 SAM/BAM/CRAM format. However, users should make sure that they align
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
950 against the indices generated by 'rsem-prepare-reference' and the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
951 alignment file satisfies the requirements mentioned in ARGUMENTS
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
952 section.
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parents:
diff changeset
953
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diff changeset
954 One simple way to make the alignment file satisfying RSEM's requirements
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
955 is to use the 'convert-sam-for-rsem' script. This script accepts
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
956 SAM/BAM/CRAM files as input and outputs a BAM file. For example, type
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
957 the following command to convert a SAM file, 'input.sam', to a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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parents:
diff changeset
958 ready-for-use BAM file, 'input_for_rsem.bam':
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parents:
diff changeset
959
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diff changeset
960 convert-sam-for-rsem input.sam input_for_rsem
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parents:
diff changeset
961
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parents:
diff changeset
962 For details, please refer to 'convert-sam-for-rsem's documentation page.
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963
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964 NOTES
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diff changeset
965 1. Users must run 'rsem-prepare-reference' with the appropriate
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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966 reference before using this program.
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967
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diff changeset
968 2. For single-end data, it is strongly recommended that the user provide
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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969 the fragment length distribution parameters (--fragment-length-mean and
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diff changeset
970 --fragment-length-sd). For paired-end data, RSEM will automatically
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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971 learn a fragment length distribution from the data.
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972
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diff changeset
973 3. Some aligner parameters have default values different from their
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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974 original settings.
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975
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976 4. With the '--calc-pme' option, posterior mean estimates will be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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977 calculated in addition to maximum likelihood estimates.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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978
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979 5. With the '--calc-ci' option, 95% credibility intervals and posterior
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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980 mean estimates will be calculated in addition to maximum likelihood
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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981 estimates.
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982
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983 6. The temporary directory and all intermediate files will be removed
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984 when RSEM finishes unless '--keep-intermediate-files' is specified.
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diff changeset
985
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986 With the '--run-pRSEM' option and associated options (see section
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
987 'PRIOR-ENHANCED RSEM OPTIONS' above for details), prior-enhanced RSEM
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diff changeset
988 will be running. Prior parameters will be learned from supplied external
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
989 data set(s) and assigned as initial pseudo-counts for isoforms in the
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diff changeset
990 corresponding partition for Gibbs sampling.
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991
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992 OUTPUT
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993 sample_name.isoforms.results
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
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diff changeset
994 File containing isoform level expression estimates. The first line
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
995 contains column names separated by the tab character. The format of
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
996 each line in the rest of this file is:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
997
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
998 transcript_id gene_id length effective_length expected_count TPM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
999 FPKM IsoPct [posterior_mean_count
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1000 posterior_standard_deviation_of_count pme_TPM pme_FPKM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1001 IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1002 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1003 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1004
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1005 Fields are separated by the tab character. Fields within "[]" are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1006 optional. They will not be presented if neither '--calc-pme' nor
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1007 '--calc-ci' is set.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1008
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1009 'transcript_id' is the transcript name of this transcript. 'gene_id'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1010 is the gene name of the gene which this transcript belongs to
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1011 (denote this gene as its parent gene). If no gene information is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1012 provided, 'gene_id' and 'transcript_id' are the same.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1013
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1014 'length' is this transcript's sequence length (poly(A) tail is not
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1015 counted). 'effective_length' counts only the positions that can
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1016 generate a valid fragment. If no poly(A) tail is added,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1017 'effective_length' is equal to transcript length - mean fragment
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1018 length + 1. If one transcript's effective length is less than 1,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1019 this transcript's both effective length and abundance estimates are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1020 set to 0.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1021
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1022 'expected_count' is the sum of the posterior probability of each
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1023 read comes from this transcript over all reads. Because 1) each read
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1024 aligning to this transcript has a probability of being generated
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1025 from background noise; 2) RSEM may filter some alignable low quality
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1026 reads, the sum of expected counts for all transcript are generally
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1027 less than the total number of reads aligned.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1028
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1029 'TPM' stands for Transcripts Per Million. It is a relative measure
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1030 of transcript abundance. The sum of all transcripts' TPM is 1
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1031 million. 'FPKM' stands for Fragments Per Kilobase of transcript per
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1032 Million mapped reads. It is another relative measure of transcript
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1033 abundance. If we define l_bar be the mean transcript length in a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1034 sample, which can be calculated as
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1035
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1036 l_bar = \sum_i TPM_i / 10^6 * effective_length_i (i goes through
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1037 every transcript),
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1038
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1039 the following equation is hold:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1040
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1041 FPKM_i = 10^3 / l_bar * TPM_i.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1042
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1043 We can see that the sum of FPKM is not a constant across samples.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1044
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1045 'IsoPct' stands for isoform percentage. It is the percentage of this
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1046 transcript's abandunce over its parent gene's abandunce. If its
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1047 parent gene has only one isoform or the gene information is not
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1048 provided, this field will be set to 100.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1049
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1050 'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1051 estimates calculated by RSEM's Gibbs sampler.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1052 'posterior_standard_deviation_of_count' is the posterior standard
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1053 deviation of counts. 'IsoPct_from_pme_TPM' is the isoform percentage
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1054 calculated from 'pme_TPM' values.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1055
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1056 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1057 and 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1058 credibility intervals for TPM and FPKM values. The bounds are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1059 inclusive (i.e. [l, u]).
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1060
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1061 'TPM_coefficient_of_quartile_variation' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1062 'FPKM_coefficient_of_quartile_variation' are coefficients of
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1063 quartile variation (CQV) for TPM and FPKM values. CQV is a robust
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1064 way of measuring the ratio between the standard deviation and the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1065 mean. It is defined as
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1066
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1067 CQV := (Q3 - Q1) / (Q3 + Q1),
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1068
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1069 where Q1 and Q3 are the first and third quartiles.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1070
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1071 sample_name.genes.results
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1072 File containing gene level expression estimates. The first line
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1073 contains column names separated by the tab character. The format of
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1074 each line in the rest of this file is:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1075
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1076 gene_id transcript_id(s) length effective_length expected_count TPM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1077 FPKM [posterior_mean_count posterior_standard_deviation_of_count
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1078 pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1079 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1080 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1081
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1082 Fields are separated by the tab character. Fields within "[]" are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1083 optional. They will not be presented if neither '--calc-pme' nor
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1084 '--calc-ci' is set.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1085
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1086 'transcript_id(s)' is a comma-separated list of transcript_ids
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1087 belonging to this gene. If no gene information is provided,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1088 'gene_id' and 'transcript_id(s)' are identical (the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1089 'transcript_id').
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1090
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1091 A gene's 'length' and 'effective_length' are defined as the weighted
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1092 average of its transcripts' lengths and effective lengths (weighted
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1093 by 'IsoPct'). A gene's abundance estimates are just the sum of its
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1094 transcripts' abundance estimates.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1095
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1096 sample_name.alleles.results
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1097 Only generated when the RSEM references are built with
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1098 allele-specific transcripts.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1099
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1100 This file contains allele level expression estimates for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1101 allele-specific expression calculation. The first line contains
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1102 column names separated by the tab character. The format of each line
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1103 in the rest of this file is:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1104
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1105 allele_id transcript_id gene_id length effective_length
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1106 expected_count TPM FPKM AlleleIsoPct AlleleGenePct
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1107 [posterior_mean_count posterior_standard_deviation_of_count pme_TPM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1108 pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1109 TPM_ci_lower_bound TPM_ci_upper_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1110 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1111 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1112
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1113 Fields are separated by the tab character. Fields within "[]" are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1114 optional. They will not be presented if neither '--calc-pme' nor
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1115 '--calc-ci' is set.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1116
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1117 'allele_id' is the allele-specific name of this allele-specific
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1118 transcript.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1119
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1120 'AlleleIsoPct' stands for allele-specific percentage on isoform
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1121 level. It is the percentage of this allele-specific transcript's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1122 abundance over its parent transcript's abundance. If its parent
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1123 transcript has only one allele variant form, this field will be set
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1124 to 100.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1125
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1126 'AlleleGenePct' stands for allele-specific percentage on gene level.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1127 It is the percentage of this allele-specific transcript's abundance
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1128 over its parent gene's abundance.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1129
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1130 'AlleleIsoPct_from_pme_TPM' and 'AlleleGenePct_from_pme_TPM' have
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1131 similar meanings. They are calculated based on posterior mean
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1132 estimates.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1133
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1134 Please note that if this file is present, the fields 'length' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1135 'effective_length' in 'sample_name.isoforms.results' should be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1136 interpreted similarly as the corresponding definitions in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1137 'sample_name.genes.results'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1138
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1139 sample_name.transcript.bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1140 Only generated when --no-bam-output is not specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1141
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1142 'sample_name.transcript.bam' is a BAM-formatted file of read
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1143 alignments in transcript coordinates. The MAPQ field of each
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1144 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1145 where w is the posterior probability of that alignment being the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1146 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1147 where value is a single precision floating number representing the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1148 posterior probability. Because this file contains all alignment
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1149 lines produced by bowtie or user-specified aligners, it can also be
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1150 used as a replacement of the aligner generated BAM/SAM file.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1151
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1152 sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1153 Only generated when --no-bam-output is not specified and --sort-bam-by-coordinate is specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1154
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1155 'sample_name.transcript.sorted.bam' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1156 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1157 indices generated by samtools (included in RSEM package).
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1158
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1159 sample_name.genome.bam
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1160 Only generated when --no-bam-output is not specified and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1161 --output-genome-bam is specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1162
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1163 'sample_name.genome.bam' is a BAM-formatted file of read alignments
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1164 in genomic coordinates. Alignments of reads that have identical
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1165 genomic coordinates (i.e., alignments to different isoforms that
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1166 share the same genomic region) are collapsed into one alignment. The
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1167 MAPQ field of each alignment is set to min(100, floor(-10 *
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1168 log10(1.0 - w) + 0.5)), where w is the posterior probability of that
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1169 alignment being the true mapping of a read. In addition, RSEM pads a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1170 new tag ZW:f:value, where value is a single precision floating
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1171 number representing the posterior probability. If an alignment is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1172 spliced, a XS:A:value tag is also added, where value is either '+'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1173 or '-' indicating the strand of the transcript it aligns to.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1174
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1175 sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1176 Only generated when --no-bam-output is not specified, and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1177 --sort-bam-by-coordinate and --output-genome-bam are specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1178
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1179 'sample_name.genome.sorted.bam' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1180 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1181 indices generated by samtools (included in RSEM package).
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1182
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1183 sample_name.time
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1184 Only generated when --time is specified.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1185
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1186 It contains time (in seconds) consumed by aligning reads, estimating
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1187 expression levels and calculating credibility intervals.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1188
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1189 sample_name.stat
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1190 This is a folder instead of a file. All model related statistics are
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1191 stored in this folder. Use 'rsem-plot-model' can generate plots
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1192 using this folder.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1193
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1194 'sample_name.stat/sample_name.cnt' contains alignment statistics.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1195 The format and meanings of each field are described in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1196 'cnt_file_description.txt' under RSEM directory.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1197
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1198 'sample_name.stat/sample_name.model' stores RNA-Seq model parameters
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1199 learned from the data. The format and meanings of each filed of this
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1200 file are described in 'model_file_description.txt' under RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1201 directory.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1202
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1203 The following four output files will be generated only by
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1204 prior-enhanced RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1205
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1206 - 'sample_name.stat/sample_name_prsem.all_tr_features'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1207 It stores isofrom features for deriving and assigning pRSEM prior.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1208 The first line is a header and the rest is one isoform per line.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1209 The description for each column is:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1210
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1211 * trid: transcript ID from input annotation
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1212
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1213 * geneid: gene ID from input anntation
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1214
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1215 * chrom: isoform's chromosome name
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1216
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1217 * strand: isoform's strand name
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1218
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1219 * start: isoform's end with the lowest genomic loci
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1220
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1221 * end: isoform's end with the highest genomic loci
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1222
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1223 * tss_mpp: average mappability of [TSS-500bp, TSS+500bp], where
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1224 TSS is isoform's transcription start site, i.e. 5'-end
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1225
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1226 * body_mpp: average mappability of (TSS+500bp, TES-500bp), where
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1227 TES is isoform's transcription end site, i.e. 3'-end
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1228
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1229 * tes_mpp: average mappability of [TES-500bp, TES+500bp]
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1230
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1231 * pme_count: isoform's fragment or read count from RSEM's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1232 posterior mean estimates
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1233
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1234 * tss: isoform's TSS loci
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1235
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1236 * tss_pk: equal to 1 if isoform's [TSS-500bp, TSS+500bp] region
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1237 overlaps with a RNA Pol II peak; 0 otherwise
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1238
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1239 * is_training: equal to 1 if isoform is in the training set where
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1240 Pol II prior is learned; 0 otherwise
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1241
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1242 - 'sample_name.stat/sample_name_prsem.all_tr_prior'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1243 It stores prior parameters for every isoform. This file does not
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1244 have a header. Each line contains a prior parameter and an
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1245 isoform's transcript ID delimited by " # ".
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1246
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1247 - 'sample_name.stat/sample_name_uniform_prior_1.isoforms.results'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1248 RSEM's posterior mean estimates on the isoform level with an
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1249 initial pseudo-count of one for every isoform. It is in the same
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1250 format as the 'sample_name.isoforms.results'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1251
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1252 - 'sample_name.stat/sample_name_uniform_prior_1.genes.results'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1253 RSEM's posterior mean estimates on the gene level with an initial
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1254 pseudo-count of one for every isoform. It is in the same format as
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1255 the 'sample_name.genes.results'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1256
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1257 When learning prior from multiple external data sets in
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1258 prior-enhanced RSEM, two additional output files will be generated.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1259
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1260 - 'sample_name.stat/sample_name.pval_LL'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1261 It stores a p-value and a log-likelihood. The p-value indicates
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1262 whether the combination of multiple complementary data sets is
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1263 informative for RNA-seq quantification. The log-likelihood shows
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1264 how well pRSEM's Dirichlet-multinomial model fits the read counts
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1265 of partitioned training set isoforms.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1266
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1267 - 'sample_name.stat/sample_name.lgt_mdl.RData'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1268 It stores an R object named 'glmmdl', which is a logistic
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1269 regression model on the training set isoforms and multiple
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1270 external data sets.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1271
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1272 In addition, extra columns will be added to
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1273 'sample_name.stat/all_tr_features'
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1274
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1275 * is_expr: equal to 1 if isoform has an abundance &gt;= 1 TPM and a
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1276 non-zero read count from RSEM's posterior mean estimates; 0
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1277 otherwise
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1278
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1279 * "$external_data_set_basename": log10 of external data's signal at
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1280 [TSS-500, TSS+500]. Signal is the number of reads aligned within
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1281 that interval and normalized to RPKM by read depth and interval
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1282 length. It will be set to -4 if no read aligned to that interval.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1283
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1284 There are multiple columns like this one, where each represents an
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1285 external data set.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1286
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1287 * prd_expr_prob: predicted probability from logistic regression
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1288 model on whether this isoform is expressed or not. A probability
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1289 higher than 0.5 is considered as expressed
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1290
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1291 * partition: group index, to which this isoforms is partitioned
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1292
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1293 * prior: prior parameter for this isoform
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1294
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1295 EXAMPLES
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1296 Assume the path to the bowtie executables is in the user's PATH
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1297 environment variable. Reference files are under '/ref' with name
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1298 'mouse_125'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1299
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1300 1) '/data/mmliver.fq', single-end reads with quality scores. Quality
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1301 scores are encoded as for 'GA pipeline version &gt;= 1.3'. We want to use 8
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1302 threads and generate a genome BAM file. In addition, we want to append
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1303 gene/transcript names to the result files:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1304
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1305 rsem-calculate-expression --phred64-quals \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1306 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1307 --append-names \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1308 --output-genome-bam \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1309 /data/mmliver.fq \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1310 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1311 mmliver_single_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1312
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1313 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', stranded paired-end
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1314 reads with quality scores. Suppose the library is prepared using TruSeq
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1315 Stranded Kit, which means the first mate should map to the reverse
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1316 strand. Quality scores are in SANGER format. We want to use 8 threads
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1317 and do not generate a genome BAM file:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1318
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1319 rsem-calculate-expression -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1320 --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1321 --strandedness reverse \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1322 /data/mmliver_1.fq \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1323 /data/mmliver_2.fq \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1324 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1325 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1326
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1327 3) '/data/mmliver.fa', single-end reads without quality scores. We want
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1328 to use 8 threads:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1329
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1330 rsem-calculate-expression -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1331 --no-qualities \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1332 /data/mmliver.fa \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1333 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1334 mmliver_single_without_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1335
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1336 4) Data are the same as 1). This time we assume the bowtie executables
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1337 are under '/sw/bowtie'. We want to take a fragment length distribution
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1338 into consideration. We set the fragment length mean to 150 and the
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1339 standard deviation to 35. In addition to a BAM file, we also want to
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1340 generate credibility intervals. We allow RSEM to use 1GB of memory for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1341 CI calculation:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1342
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1343 rsem-calculate-expression --bowtie-path /sw/bowtie \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1344 --phred64-quals \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1345 --fragment-length-mean 150.0 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1346 --fragment-length-sd 35.0 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1347 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1348 --output-genome-bam \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1349 --calc-ci \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1350 --ci-memory 1024 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1351 /data/mmliver.fq \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1352 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1353 mmliver_single_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1354
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1355 5) '/data/mmliver_paired_end_quals.bam', BAM-formatted alignments for
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1356 paired-end reads with quality scores. We want to use 8 threads:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1357
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1358 rsem-calculate-expression --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1359 --alignments \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1360 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1361 /data/mmliver_paired_end_quals.bam \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1362 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1363 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1364
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1365 6) '/data/mmliver_1.fq.gz' and '/data/mmliver_2.fq.gz', paired-end reads
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1366 with quality scores and read files are compressed by gzip. We want to
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1367 use STAR to aligned reads and assume STAR executable is '/sw/STAR'.
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1368 Suppose we want to use 8 threads and do not generate a genome BAM file:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1369
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1370 rsem-calculate-expression --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1371 --star \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1372 --star-path /sw/STAR \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1373 --gzipped-read-file \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1374 --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1375 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1376 /data/mmliver_1.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1377 /data/mmliver_2.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1378 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1379 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1380
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1381 7) In the above example, suppose we want to run prior-enhanced RSEM
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1382 instead. Assuming we want to learn priors from a ChIP-seq peak file
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1383 '/data/mmlive.narrowPeak.gz':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1384
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1385 rsem-calculate-expression --star \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1386 --star-path /sw/STAR \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1387 --gzipped-read-file \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1388 --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1389 --calc-pme \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1390 --run-pRSEM \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1391 --chipseq-peak-file /data/mmliver.narrowPeak.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1392 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1393 /data/mmliver_1.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1394 /data/mmliver_2.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1395 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1396 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1397
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1398 8) Similar to the example in 7), suppose we want to use the partition
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1399 model 'pk_lm2nopk' (partitioning isoforms by Pol II TSS peak first and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1400 then partitioning 'no TSS peak' isoforms into two bins by a linear
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1401 regression model), and we want to partition isoforms by RNA Pol II's
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1402 ChIP-seq read files '/data/mmliver_PolIIRep1.fq.gz' and
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1403 '/data/mmliver_PolIIRep2.fq.gz', and the control ChIP-seq read files
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1404 '/data/mmliver_ChIPseqCtrl.fq.gz'. Also, assuming Bowtie's executables
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1405 are under '/sw/bowtie/':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1406
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1407 rsem-calculate-expression --star \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1408 --star-path /sw/STAR \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1409 --gzipped-read-file \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1410 --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1411 --calc-pme \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1412 --run-pRSEM \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1413 --chipseq-target-read-files /data/mmliver_PolIIRep1.fq.gz,/data/mmliver_PolIIRep2.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1414 --chipseq-control-read-files /data/mmliver_ChIPseqCtrl.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1415 --partition-model pk_lm2nopk \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1416 --bowtie-path /sw/bowtie \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1417 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1418 /data/mmliver_1.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1419 /data/mmliver_2.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1420 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1421 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1422
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1423 9) Similar to the example in 8), suppose we want to derive prior from
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1424 four histone modification ChIP-seq read data sets:
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1425 '/data/H3K27Ac.fastq.gz', '/data/H3K4me1.fastq.gz',
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1426 '/data/H3K4me2.fastq.gz', and '/data/H3K4me3.fastq.gz'. Also, assuming
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1427 Bowtie's executables are under '/sw/bowtie/':
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1428
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1429 rsem-calculate-expression --star \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1430 --star-path /sw/STAR \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1431 --gzipped-read-file \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1432 --paired-end \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1433 --calc-pme \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1434 --run-pRSEM \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1435 --partition-model cmb_lgt \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1436 --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1437 --bowtie-path /sw/bowtie \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1438 -p 8 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1439 /data/mmliver_1.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1440 /data/mmliver_2.fq.gz \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1441 /ref/mouse_125 \
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1442 mmliver_paired_end_quals
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1443
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1444 </help>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1445 <citations>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1446 <citation type="doi">10.1186/1471-2105-12-323</citation>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1447 </citations>
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1448
78a1909aca3e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit f517d1dbd9f4c6fd0b37317555315c60a09451ee
artbio
parents:
diff changeset
1449 </tool>