Mercurial > repos > lparsons > rseqc

annotate RPKM_count.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_count" name="RPKM Count" 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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7
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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8 <requirements>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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9 <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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10 <expand macro="requirement_package_rseqc" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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11 </requirements>
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12
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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13 <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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15 <version_command><![CDATA[RPKM_count.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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16
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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17 <command><![CDATA[
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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18 ln -s "${input}" "local_input.bam" &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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19 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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20 RPKM_count.py -i "local_input.bam" -o output -r $refgene
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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21
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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22 #if str($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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23 -d
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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24 #if str($strand_type.pair_type) == "sd"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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25 '1++,1--,2+-,2-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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26 #else
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27 '1+-,1-+,2++,2--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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28 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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30
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31 #if str($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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32 -d
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33 #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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34 '++,--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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35 #else
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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36 '+-,-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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37 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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38 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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39
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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40 #if $multihits.skipmultihits
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41 --skip-multi-hits
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42 --mapq=$multihits.mapq
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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43 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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44
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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45 $onlyexonic
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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46 ]]>
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47 </command>
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48
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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49 <inputs>
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50 <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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51 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
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52 <conditional name="strand_type">
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53 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
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54 <option value="none">None</option>
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55 <option value="pair">Pair-End RNA-seq</option>
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56 <option value="single">Single-End RNA-seq</option>
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57 </param>
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58 <when value="pair">
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59 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
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60 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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61 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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62 </param>
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63 </when>
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64 <when value="single">
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65 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
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66 <option value="s">positive --> positive; negative --> negative</option>
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67 <option value="d">positive --> negative; negative --> positive</option>
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68 </param>
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69 </when>
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70 <when value="none"></when>
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71 </conditional>
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72
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73 <conditional name="multihits">
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74 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" />
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75 <when value="true">
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76 <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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77 </when>
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78 <when value="false" />
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79 </conditional>
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80
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81 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
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82 </inputs>
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83
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84 <outputs>
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85 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
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86 </outputs>
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87
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88 <tests>
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89 <test>
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90 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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91 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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92 <output name="outputxls" file="output_read_count.xls"/>
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93 </test>
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94 </tests>
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95
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96 <help><![CDATA[
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97 RPKM_count.py
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98 +++++++++++++
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99
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100 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM
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101 values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data,
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102 program will assign read to its parental gene according to strand rule, if you don't know the
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103 strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates
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104 should be concordant between BAM and BED files.
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105
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106 Inputs
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107 ++++++++++++++
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108
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109 Input BAM/SAM file
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110 Alignment file in BAM/SAM format.
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111
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112 Reference gene model
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113 Gene model in BED format.
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114
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115 Strand sequencing type (default=none)
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116 See Infer Experiment tool if uncertain.
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117
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118 Options
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119 ++++++++++++++
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120
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121 Skip Multiple Hit Reads
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122 Use Multiple hit reads or use only uniquely mapped reads.
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123
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124 Only use exonic reads
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125 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
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126
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127 Sample Output
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128 ++++++++++++++
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129
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130 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
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131 chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-)
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132 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
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133 chr1 29213722 29313959 NM_001166007_intron_1 0 '+' 431 4329 0.086 0.863
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134 chr1 29314417 29319841 NM_001166007_intron_2 0 '+' 31 1 0.114 0.004
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135 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000
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136 chr1 29213602 29213722 NM_001166007_exon_1 0 '+' 164 0 27.321 0.000
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137 chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175
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138 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
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139 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
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140
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141 -----
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142
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143 About RSeQC
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144 +++++++++++
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145
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146 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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147
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148 The RSeQC package is licensed under the GNU GPL v3 license.
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149
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150 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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151
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152 .. _RSeQC: http://rseqc.sourceforge.net/
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153 ]]>
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154 </help>
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155
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156 <expand macro="citations" />
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157
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158 </tool>