Mercurial > repos > nilesh > rseqc

annotate infer_experiment.xml @ 49:6b33e31bda10 draft

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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents eb339c5849bb
children 09846d5169fa
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1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="2.4galaxy1">
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2 <description>speculates how RNA-seq were configured</description>
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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7
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8 <requirements>
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9 <expand macro="requirement_package_numpy" />
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10 <expand macro="requirement_package_rseqc" />
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11 </requirements>
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13 <expand macro="stdio" />
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15 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
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17 <command><![CDATA[
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18 infer_experiment.py -i $input -r $refgene
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19 --sample-size $sample_size
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20 --mapq $mapq
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21 > $output
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22 ]]>
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23 </command>
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24
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25 <inputs>
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26 <param name="input" type="data" format="bam,sam" label="Input BAM/SAM file" help="(--input-file)"/>
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27 <param name="refgene" type="data" format="bed" label="Reference gene model in bed format" help="(--refgene)" />
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28 <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" help="(--sample-size)"/>
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29 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
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30 </inputs>
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31
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32 <outputs>
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33 <data format="txt" name="output" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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39 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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40 <output name="output" file="output.infer_experiment.txt"/>
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41 </test>
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42 </tests>
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44 <help><![CDATA[
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45 infer_experiment.py
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46 +++++++++++++++++++
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47
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48 This program is used to speculate how RNA-seq sequencing were configured, especially how
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49 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
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50 information to the underneath gene model.
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51
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52
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53 Inputs
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54 ++++++++++++++
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55
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56 Input BAM/SAM file
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57 Alignment file in BAM/SAM format.
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58
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59 Reference gene model
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60 Gene model in BED format.
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61
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62 Number of usable sampled reads (default=200000)
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63 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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64
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65 Outputs
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66 +++++++
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67
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68 For pair-end RNA-seq, there are two different
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69 ways to strand reads (such as Illumina ScriptSeq protocol):
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70
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71 1. 1++,1--,2+-,2-+
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72
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73 * read1 mapped to '+' strand indicates parental gene on '+' strand
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74 * read1 mapped to '-' strand indicates parental gene on '-' strand
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75 * read2 mapped to '+' strand indicates parental gene on '-' strand
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76 * read2 mapped to '-' strand indicates parental gene on '+' strand
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77
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78 2. 1+-,1-+,2++,2--
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79
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80 * read1 mapped to '+' strand indicates parental gene on '-' strand
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81 * read1 mapped to '-' strand indicates parental gene on '+' strand
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82 * read2 mapped to '+' strand indicates parental gene on '+' strand
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83 * read2 mapped to '-' strand indicates parental gene on '-' strand
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84
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85 For single-end RNA-seq, there are also two different ways to strand reads:
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86
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87 1. ++,--
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88
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89 * read mapped to '+' strand indicates parental gene on '+' strand
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90 * read mapped to '-' strand indicates parental gene on '-' strand
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91
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92 2. +-,-+
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93
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94 * read mapped to '+' strand indicates parental gene on '-' strand
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95 * read mapped to '-' strand indicates parental gene on '+' strand
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97
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98 Example Output
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99 ++++++++++++++
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100
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101 **Example1** ::
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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-+": 0.4992
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107 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008
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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 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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112
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113 **Example2** ::
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114
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115 ============================================================
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116 This is PairEnd Data
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117
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118 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 ::
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119 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356
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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*: 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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124
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125 **Example3** ::
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126
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127 =========================================================
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128 This is SingleEnd Data ::
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129
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130 Fraction of reads explained by "++,--": 0.9840 ::
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131 Fraction of reads explained by "+-,-+": 0.0160
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132 Fraction of reads explained by other combinations: 0.0000
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133 =========================================================
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134
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135 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
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136
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137
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138 -----
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139
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140 About RSeQC
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141 +++++++++++
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142
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143 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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144
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145 The RSeQC package is licensed under the GNU GPL v3 license.
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146
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147 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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148
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149 .. _RSeQC: http://rseqc.sourceforge.net/
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150
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151 ]]>
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152 </help>
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154 <expand macro="citations" />
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155
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156 </tool>