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comparison bam_stat.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 2f55e1d520cd
children 580ee0c4bc4e
comparison
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30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="bam_stat" name="BAM/SAM Mapping Stats"> 1 <tool id="bam_stat" name="BAM/SAM Mapping Stats" version="1.1">
2 <description> 2 <description>
3 reads mapping statistics for a provided BAM or SAM file. 3 reads mapping statistics for a provided BAM or SAM file.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.7">rseqc</requirement> 7 <requirement type="package" version="2.3.7">rseqc</requirement>
7 </requirements>s 8 </requirements>s
8 <command interpreter="python"> 9 <command>
9 bam_stat.py -i $input -q $mapqual > $output 10 bam_stat.py -i $input -q $mapqual 2> $output
10 </command> 11 </command>
11 <inputs> 12 <inputs>
12 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> 13 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
13 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" /> 14 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
14 </inputs> 15 </inputs>
15 <outputs> 16 <outputs>
16 <data format="txt" name="output" /> 17 <data format="txt" name="output" />
17 </outputs> 18 </outputs>
19 <stdio>
20 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
21 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
22 </stdio>
18 <help> 23 <help>
19 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 24 bam_stat.py
20
21 -----
22
23 About RSeQC
24 +++++++++++ 25 +++++++++++
25 26
26 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. 27 This program is used to calculate reads mapping statistics from provided BAM
27 28 file. This script determines "uniquely mapped reads" from `mapping quality`_,
28 The RSeQC package is licensed under the GNU GPL v3 license. 29 which quality the probability that a read is misplaced (Do NOT confused with
30 sequence quality, sequence quality measures the probability that a base-calling
31 was wrong) .
29 32
30 Inputs 33 Inputs
31 ++++++++++++++ 34 ++++++++++++++
32 35
33 Input BAM/SAM file 36 Input BAM/SAM file
42 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped} 45 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
43 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end) 46 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
44 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'} 47 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
45 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads} 48 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
46 49
50 -----
51
52 About RSeQC
53 +++++++++++
54
55 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.
56
57 The RSeQC package is licensed under the GNU GPL v3 license.
58
59 .. image:: http://rseqc.sourceforge.net/_static/logo.png
60
61 .. _RSeQC: http://rseqc.sourceforge.net/
62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
47 63
48 </help> 64 </help>
49 </tool> 65 </tool>