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annotate infer_experiment.xml @ 41:e1dd49718284

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Fixed tool versions
author Lance Parsons <lparsons@princeton.edu>
date Wed, 23 Jul 2014 10:52:30 -0400
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41
e1dd49718284 Fixed tool versions
Lance Parsons <lparsons@princeton.edu>
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1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="2.3.9">
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2 <description>speculates how RNA-seq were configured</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.1">numpy</requirement>
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5 <requirement type="package" version="2.3.9">rseqc</requirement>
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6 </requirements>
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7 <command>
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8 infer_experiment.py -i $input -r $refgene
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9 #if $sample_size.boolean
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10 -s $sample_size.size
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11 #end if
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12
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13 > $output
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14 </command>
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15 <stdio>
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16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
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17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
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18 </stdio>
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19 <inputs>
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20 <param name="input" type="data" format="bam,sam" label="Input BAM/SAM file" />
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21 <param name="refgene" type="data" format="bed" label="Reference gene model in bed format" />
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22 <conditional name="sample_size">
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23 <param name="boolean" type="boolean" label="Modify usable sampled reads" value="false" />
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24 <when value="true">
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25 <param name="size" type="integer" label="Number of usable sampled reads (default = 200000)" value="200000" />
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26 </when>
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27 </conditional>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="output" />
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31 </outputs>
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32 <help>
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33 infer_experiment.py
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34 +++++++++++++++++++
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35
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36 This program is used to speculate how RNA-seq sequencing were configured, especially how
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37 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
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38 information to the underneath gene model.
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39
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40
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41 Inputs
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42 ++++++++++++++
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43
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44 Input BAM/SAM file
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45 Alignment file in BAM/SAM format.
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46
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47 Reference gene model
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48 Gene model in BED format.
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49
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50 Number of usable sampled reads (default=200000)
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51 Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower.
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52
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53 Outputs
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54 +++++++
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55
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56 For pair-end RNA-seq, there are two different
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57 ways to strand reads (such as Illumina ScriptSeq protocol):
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58
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59 1. 1++,1--,2+-,2-+
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60
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61 * read1 mapped to '+' strand indicates parental gene on '+' strand
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62 * read1 mapped to '-' strand indicates parental gene on '-' strand
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63 * read2 mapped to '+' strand indicates parental gene on '-' strand
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64 * read2 mapped to '-' strand indicates parental gene on '+' strand
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65
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66 2. 1+-,1-+,2++,2--
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67
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68 * read1 mapped to '+' strand indicates parental gene on '-' strand
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69 * read1 mapped to '-' strand indicates parental gene on '+' strand
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70 * read2 mapped to '+' strand indicates parental gene on '+' strand
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71 * read2 mapped to '-' strand indicates parental gene on '-' strand
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72
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73 For single-end RNA-seq, there are also two different ways to strand reads:
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74
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75 1. ++,--
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76
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77 * read mapped to '+' strand indicates parental gene on '+' strand
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78 * read mapped to '-' strand indicates parental gene on '-' strand
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79
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80 2. +-,-+
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81
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82 * read mapped to '+' strand indicates parental gene on '-' strand
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83 * read mapped to '-' strand indicates parental gene on '+' strand
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84
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85
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86 Example Output
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87 ++++++++++++++
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88
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89 **Example1** ::
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90
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91 =========================================================
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92 This is PairEnd Data ::
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93
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94 Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992
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95 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008
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96 Fraction of reads explained by other combinations: 0.0000
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97 =========================================================
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98
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99 *Conclusion*: We can infer that this is NOT a strand specific because 50% of reads can be explained by "1++,1--,2+-,2-+", while the other 50% can be explained by "1+-,1-+,2++,2--".
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100
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101 **Example2** ::
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102
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103 ============================================================
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104 This is PairEnd Data
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105
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106 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 ::
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107 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356
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108 Fraction of reads explained by other combinations: 0.0000
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109 ============================================================
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110
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111 *Conclusion*: We can infer that this is a strand-specific RNA-seq data. strandness of read1 is consistent with that of gene model, while strandness of read2 is opposite to the strand of reference gene model.
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112
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113 **Example3** ::
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114
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115 =========================================================
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116 This is SingleEnd Data ::
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117
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118 Fraction of reads explained by "++,--": 0.9840 ::
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119 Fraction of reads explained by "+-,-+": 0.0160
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120 Fraction of reads explained by other combinations: 0.0000
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121 =========================================================
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122
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123 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
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124
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125
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126 -----
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127
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128 About RSeQC
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129 +++++++++++
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130
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131 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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132
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133 The RSeQC package is licensed under the GNU GPL v3 license.
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134
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135 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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136
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137 .. _RSeQC: http://rseqc.sourceforge.net/
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138
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139
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140 </help>
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141 </tool>