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comparison geneBody_coverage.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents ce0995c33291
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="geneBody_coverage" name="Gene Body Converage (BAM)"> 1 <tool id="geneBody_coverage" name="Gene Body Converage (BAM)" version="1.1">
2 <description> 2 <description>
3 Read coverage over gene body. 3 Read coverage over gene body.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement> 6 <requirement type="package" version="2.11.0">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
7 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
8 </requirements> 9 </requirements>
9 <command interpreter="python"> 10 <command>
10 geneBody_coverage.py -i $input -r $refgene -o output 11 geneBody_coverage.py -i $input -r $refgene -o output
11 </command> 12 </command>
12 <inputs> 13 <inputs>
13 <param name="input" type="data" label="Input .bam file" format="bam" /> 14 <param name="input" type="data" label="Input .bam file" format="bam" />
14 <param name="refgene" type="data" label="Reference Genome" format="bed" /> 15 <param name="refgene" type="data" label="Reference Genome" format="bed" />
15 </inputs> 16 </inputs>
16 <outputs> 17 <outputs>
17 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" /> 18 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
18 <data name="outputr" format="r" from_work_dir="output.geneBodyCoverage_plot.r" /> 19 <data name="outputr" format="r" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
19 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" /> 20 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
20 </outputs> 21 </outputs>
22 <stdio>
23 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
24 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
25 </stdio>
21 <help> 26 <help>
22 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 27 geneBody_coverage.py
28 ++++++++++++++++++++
23 29
24 ----- 30 Read coverage over gene body. This module is used to check if reads coverage is uniform and
25 31 if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the
26 About RSeQC 32 number of reads covering each nucleotide position. Finally, it generates a plot illustrating
27 +++++++++++ 33 the coverage profile along the gene body. NOTE: this module requires lots of memory for large
28 34 BAM files, because it load the entire BAM file into memory. We add another script
29 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. 35 "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input.
30 36 It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
31 The RSeQC package is licensed under the GNU GPL v3 license.
32 37
33 Inputs 38 Inputs
34 ++++++++++++++ 39 ++++++++++++++
35 40
36 Input BAM/SAM file 41 Input BAM/SAM file
44 ++++++++++++++ 49 ++++++++++++++
45 50
46 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig. 51 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
47 52
48 Example output: 53 Example output:
49 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.png 54 .. image:: http://rseqc.sourceforge.net/_images/geneBody_coverage.png
55 :height: 600 px
56 :width: 600 px
57 :scale: 80 %
58
59
60 -----
61
62 About RSeQC
63 +++++++++++
64
65 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.
66
67 The RSeQC package is licensed under the GNU GPL v3 license.
68
69 .. image:: http://rseqc.sourceforge.net/_static/logo.png
70
71 .. _RSeQC: http://rseqc.sourceforge.net/
50 72
51 73
52 74
53 </help> 75 </help>
54 </tool> 76 </tool>