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comparison read_NVC.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 907d4b021ff6
children 580ee0c4bc4e
comparison
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30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="read_NVC" name="Read NVC"> 1 <tool id="read_NVC" name="Read NVC" version="1.1">
2 <description>to check the nucleotide composition bias</description> 2 <description>to check the nucleotide composition bias</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.15.1">R</requirement> 4 <requirement type="package" version="2.11.0">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements> 7 </requirements>
7 <command interpreter="python"> read_NVC.py -i $input -o output 8 <command> read_NVC.py -i $input -o output
8 9
9 #if $nx 10 #if $nx
10 -x 11 -x
11 #end if 12 #end if
12 </command> 13 </command>
13 <inputs> 14 <inputs>
14 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 15 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
15 <param name="nx" type="boolean" label="Include N,X in NVC plot" value="false" /> 16 <param name="nx" type="boolean" label="Include N,X in NVC plot" value="false" />
16 </inputs> 17 </inputs>
17 <outputs> 18 <outputs>
18 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls"/> 19 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
19 <data format="r" name="outputr" from_work_dir="output.NVC_plot.r" /> 20 <data format="r" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
20 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" /> 21 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
21 </outputs> 22 </outputs>
23 <stdio>
24 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
25 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
26 </stdio>
22 <help> 27 <help>
23 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 28 read_NVC.py
24
25 -----
26
27 About RSeQC
28 +++++++++++ 29 +++++++++++
29 30
30 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. 31 This module is used to check the nucleotide composition bias. Due to random priming, certain
32 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
33 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
34 reads together, then calculating nucleotide composition for each position of read
35 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
36 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
31 37
32 The RSeQC package is licensed under the GNU GPL v3 license. 38 NOTE: this program expect a fixed read length
33 39
34 Inputs 40 Inputs
35 ++++++++++++++ 41 ++++++++++++++
36 42
37 Input BAM/SAM file 43 Input BAM/SAM file
49 1. output.NVC.xls: plain text file, each row is position of read (or sequencing cycle), each column is nucleotide (A,C,G,T,N,X) 55 1. output.NVC.xls: plain text file, each row is position of read (or sequencing cycle), each column is nucleotide (A,C,G,T,N,X)
50 2. output.NVC_plot.r: R script to generate NVC plot. 56 2. output.NVC_plot.r: R script to generate NVC plot.
51 3. output.NVC_plot.pdf: NVC plot. 57 3. output.NVC_plot.pdf: NVC plot.
52 58
53 59
54 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/NVC_plot.png 60 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png
61 :height: 600 px
62 :width: 600 px
63 :scale: 80 %
64
65 -----
66
67 About RSeQC
68 +++++++++++
69
70 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.
71
72 The RSeQC package is licensed under the GNU GPL v3 license.
73
74 .. image:: http://rseqc.sourceforge.net/_static/logo.png
75
76 .. _RSeQC: http://rseqc.sourceforge.net/
77
55 78
56 </help> 79 </help>
57 </tool> 80 </tool>