Mercurial > repos > lparsons > rseqc

annotate RPKM_saturation.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="2.4galaxy1">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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3
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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4 <macros>
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5 <import>rseqc_macros.xml</import>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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6 </macros>
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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8 <requirements>
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9 <expand macro="requirement_package_r" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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10 <expand macro="requirement_package_numpy" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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11 <expand macro="requirement_package_rseqc" />
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12 </requirements>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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13
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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14 <expand macro="stdio" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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16 <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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18 <command><![CDATA[
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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19 RPKM_saturation.py -i $input -o output -r $refgene
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21 #if str($strand_type.strand_specific) == "pair"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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22 -d
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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23 #if str($strand_type.pair_type) == "sd"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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24 '1++,1--,2+-,2-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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25 #else
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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26 '1+-,1-+,2++,2--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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27 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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28 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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30 #if str($strand_type.strand_specific) == "single"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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31 -d
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32 #if str($strand_type.single_type) == "s"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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33 '++,--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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34 #else
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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35 '+-,-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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36 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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37 #end if
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38
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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39 -l $percentileFloor -u $percentileCeiling -s $percentileStep -c $rpkmCutoff
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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40 ]]>
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41 </command>
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42
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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43 <inputs>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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44 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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45 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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46 <conditional name="strand_type">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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47 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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48 <option value="none">None</option>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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49 <option value="pair">Pair-End RNA-seq</option>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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50 <option value="single">Single-End RNA-seq</option>
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51 </param>
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52 <when value="pair">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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53 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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54 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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55 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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56 </param>
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57 </when>
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58 <when value="single">
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59 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
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60 <option value="s">positive --> positive; negative --> negative</option>
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61 <option value="d">positive --> negative; negative --> positive</option>
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62 </param>
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63 </when>
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64 <when value="none"></when>
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65 </conditional>
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66 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
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67 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
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68 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />
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69 <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" />
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70 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
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71 </inputs>
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72
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73 <outputs>
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74 <data format="xls" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string} (RPKM XLS)"/>
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75 <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count XLS)"/>
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76 <data format="txt" name="outputr" from_work_dir="output.saturation.r" label="${tool.name} on ${on_string} (R Script)"/>
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77 <data format="pdf" name="outputpdf" from_work_dir="output.saturation.pdf" label="${tool.name} on ${on_string} (PDF)"/>
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78 </outputs>
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79
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80 <!-- Unable to succefully run this script with test data
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81 <tests>
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82 <test>
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83 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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84 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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85 <output name="outputxls" file="output.eRPKM.xls"/>
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86 <output name="outputrawxls" file="output.rawCount.xls"/>
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87 <output name="outputr" file="output.saturation.r"/>
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88 </test>
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89 </tests>
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90 -->
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91
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92 <help><![CDATA[
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93 RPKM_saturation.py
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94 ++++++++++++++++++
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95
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96 The precision of any sample statitics (RPKM) is affected by sample size (sequencing depth);
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97 \'resampling\' or \'jackknifing\' is a method to estimate the precision of sample statistics by
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98 using subsets of available data. This module will resample a series of subsets from total RNA
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99 reads and then calculate RPKM value using each subset. By doing this we are able to check if
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100 the current sequencing depth was saturated or not (or if the RPKM values were stable or not)
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101 in terms of genes' expression estimation. If sequencing depth was saturated, the estimated
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102 RPKM value will be stationary or reproducible. By default, this module will calculate 20
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103 RPKM values (using 5%, 10%, ... , 95%,100% of total reads) for each transcripts.
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104
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105 In the output figure, Y axis is "Percent Relative Error" or "Percent Error" which is used
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106 to measures how the RPKM estimated from subset of reads (i.e. RPKMobs) deviates from real
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107 expression level (i.e. RPKMreal). However, in practice one cannot know the RPKMreal. As a
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108 proxy, we use the RPKM estimated from total reads to approximate RPKMreal.
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109
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110 .. image:: http://rseqc.sourceforge.net/_images/RelativeError.png
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111 :height: 80 px
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112 :width: 400 px
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113 :scale: 100 %
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114
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115 Inputs
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116 ++++++++++++++
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117
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118 Input BAM/SAM file
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119 Alignment file in BAM/SAM format.
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120
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121 Reference gene model
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122 Gene model in BED format.
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123
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124 Strand sequencing type (default=none)
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125 See Infer Experiment tool if uncertain.
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126
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127 Options
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128 ++++++++++++++
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129
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130 Skip Multiple Hit Reads
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131 Use Multiple hit reads or use only uniquely mapped reads.
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132
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133 Only use exonic reads
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134 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
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135
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136 Output
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137 ++++++++++++++
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138
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139 1. output..eRPKM.xls: RPKM values for each transcript
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140 2. output.rawCount.xls: Raw count for each transcript
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141 3. output.saturation.r: R script to generate plot
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142 4. output.saturation.pdf:
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143
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144 .. image:: http://rseqc.sourceforge.net/_images/saturation.png
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145 :height: 600 px
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146 :width: 600 px
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147 :scale: 80 %
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148
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149 - All transcripts were sorted in ascending order according to expression level (RPKM). Then they are divided into 4 groups:
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150 1. Q1 (0-25%): Transcripts with expression level ranked below 25 percentile.
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151 2. Q2 (25-50%): Transcripts with expression level ranked between 25 percentile and 50 percentile.
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152 3. Q3 (50-75%): Transcripts with expression level ranked between 50 percentile and 75 percentile.
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153 4. Q4 (75-100%): Transcripts with expression level ranked above 75 percentile.
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154 - BAM/SAM file containing more than 100 million alignments will make module very slow.
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155 - Follow example below to visualize a particular transcript (using R console)::
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156
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157 pdf("xxx.pdf") #starts the graphics device driver for producing PDF graphics
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158 x &lt;- seq(5,100,5) #resampling percentage (5,10,15,...,100)
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159 rpkm &lt;- c(32.95,35.43,35.15,36.04,36.41,37.76,38.96,38.62,37.81,38.14,37.97,38.58,38.59,38.54,38.67, 38.67,38.87,38.68, 38.42, 38.23) #Paste RPKM values calculated from each subsets
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160 scatter.smooth(x,100*abs(rpkm-rpkm[length(rpkm)])/(rpkm[length(rpkm)]),type="p",ylab="Precent Relative Error",xlab="Resampling Percentage")
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161 dev.off() #close graphical device
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162
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163 .. image:: http://rseqc.sourceforge.net/_images/saturation_eg.png
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164 :height: 600 px
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165 :width: 600 px
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166 :scale: 80 %
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167
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168 -----
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169
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170 About RSeQC
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171 +++++++++++
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172
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173 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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174
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175 The RSeQC package is licensed under the GNU GPL v3 license.
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176
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177 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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178
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179 .. _RSeQC: http://rseqc.sourceforge.net/
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180 ]]>
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181 </help>
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182
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183 <expand macro="citations" />
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184
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parents:
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185 </tool>