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comparison read_quality.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_quality" name="Read Quality"> 1 <tool id="read_quality" name="Read Quality" version="1.1">
2 <description>determines Phred quality score</description> 2 <description>determines Phred quality score</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_quality.py -i $input -o output -r $reduce 8 <command> read_quality.py -i $input -o output -r $reduce
8 </command> 9 </command>
9 <inputs> 10 <inputs>
10 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
11 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> 12 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" />
12 </inputs> 13 </inputs>
13 <outputs> 14 <outputs>
14 <data format="r" name="outputr" from_work_dir="output.qual.r" /> 15 <data format="r" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
15 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" /> 16 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
16 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" /> 17 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
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 read_quality.py
25 +++++++++++++++
20 26
21 ----- 27 According to SAM specification, if Q is the character to represent "base calling quality"
22 28 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
23 About RSeQC 29 returns an integer representing the Unicode code point of the character when the argument
24 +++++++++++ 30 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
25 31 to measure "reliability" of base-calling, for example, phred quality score of 20 means
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. 32 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
27 33 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
28 The RSeQC package is licensed under the GNU GPL v3 license. 34 here P is probability that base-calling is wrong.
29 35
30 Inputs 36 Inputs
31 ++++++++++++++ 37 ++++++++++++++
32 38
33 Input BAM/SAM file 39 Input BAM/SAM file
39 Output 45 Output
40 ++++++++++++++ 46 ++++++++++++++
41 47
42 1. output.qual.r 48 1. output.qual.r
43 2. output.qual.boxplot.pdf 49 2. output.qual.boxplot.pdf
44 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.plot.png 50 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
51 :height: 600 px
52 :width: 600 px
53 :scale: 80 %
45 3. output.qual.heatmap.pdf 54 3. output.qual.heatmap.pdf
46 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.heatmap.png 55 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
47 use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") 56 :height: 600 px
57 :width: 600 px
58 :scale: 80 %
59
60 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
61
62 -----
63
64 About RSeQC
65 +++++++++++
66
67 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.
68
69 The RSeQC package is licensed under the GNU GPL v3 license.
70
71 .. image:: http://rseqc.sourceforge.net/_static/logo.png
72
73 .. _RSeQC: http://rseqc.sourceforge.net/
74
48 75
49 </help> 76 </help>
50 </tool> 77 </tool>