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comparison geneBody_coverage2.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 64dc986da596
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="geneBody_coverage" name="Gene Body Converage (Bigwig)"> 1 <tool id="geneBody_coverage2" name="Gene Body Converage (Bigwig)" 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_coverage2.py -i $input -r $refgene -o output 11 geneBody_coverage2.py -i $input -r $refgene -o output
11 </command> 12 </command>
12 <inputs> 13 <inputs>
13 <param name="input" type="data" label="Input bigwig file" format="bigwig" /> 14 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
14 <param name="refgene" type="data" label="Reference Genome" format="bed" /> 15 <param name="refgene" type="data" label="Reference Genome" format="bed" />
15 </inputs> 16 </inputs>
16 <outputs> 17 <outputs>
17 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" /> 18 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${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_coverage2.py
28 +++++++++++++++++++++
23 29
24 ----- 30 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
31 requires much less memory. The BigWig file could be arbitrarily large.
25 32
26 About RSeQC
27 +++++++++++
28
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.
30
31 The RSeQC package is licensed under the GNU GPL v3 license.
32 33
33 Inputs 34 Inputs
34 ++++++++++++++ 35 ++++++++++++++
35 36
36 Input BAM/SAM file 37 Input BAM/SAM file
44 ++++++++++++++ 45 ++++++++++++++
45 46
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. 47 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 48
48 Example output: 49 Example output:
49 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.png 50 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.png
51 :height: 600 px
52 :width: 600 px
53 :scale: 80 %
54
55 -----
56
57 About RSeQC
58 +++++++++++
59
60 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.
61
62 The RSeQC package is licensed under the GNU GPL v3 license.
63
64 .. image:: http://rseqc.sourceforge.net/_static/logo.png
65
66 .. _RSeQC: http://rseqc.sourceforge.net/
50 67
51 68
52 69
53 </help> 70 </help>
54 </tool> 71 </tool>