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comparison junction_saturation.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents d064a3014efd
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="junction_saturation" name="Junction Saturation"> 1 <tool id="junction_saturation" name="Junction Saturation" version="1.1">
2 <description>detects splice junctions from each subset and compares them to reference gene model</description> 2 <description>detects splice junctions from each subset and compares them to reference gene model</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"> junction_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice 8 <command> junction_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
8 9
9 #if $percentiles.specifyPercentiles 10 #if $percentiles.specifyPercentiles
10 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep 11 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
11 #end if 12 #end if
12 13
24 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" /> 25 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
25 </when> 26 </when>
26 </conditional> 27 </conditional>
27 </inputs> 28 </inputs>
28 <outputs> 29 <outputs>
29 <data format="r" name="outputr" from_work_dir="output.junctionSaturation_plot.r"/> 30 <data format="r" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
30 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf"/> 31 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
31 </outputs> 32 </outputs>
33 <stdio>
34 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
35 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
36 </stdio>
32 <help> 37 <help>
33 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 38 junction_saturation.py
39 ++++++++++++++++++++++
34 40
35 ----- 41 It's very important to check if current sequencing depth is deep enough to perform
36 42 alternative splicing analyses. For a well annotated organism, the number of expressed genes
37 About RSeQC 43 in particular tissue is almost fixed so the number of splice junctions is also fixed. The fixed
38 +++++++++++ 44 splice junctions can be predetermined from reference gene model. All (annotated) splice
39 45 junctions should be rediscovered from a saturated RNA-seq data, otherwise, downstream
40 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. 46 alternative splicing analysis is problematic because low abundance splice junctions are
41 47 missing. This module checks for saturation by resampling 5%, 10%, 15%, ..., 95% of total
42 The RSeQC package is licensed under the GNU GPL v3 license. 48 alignments from BAM or SAM file, and then detects splice junctions from each subset and
49 compares them to reference gene model.
43 50
44 Inputs 51 Inputs
45 ++++++++++++++ 52 ++++++++++++++
46 53
47 Input BAM/SAM file 54 Input BAM/SAM file
63 ++++++++++++++ 70 ++++++++++++++
64 71
65 1. output.junctionSaturation_plot.r: R script to generate plot 72 1. output.junctionSaturation_plot.r: R script to generate plot
66 2. output.junctionSaturation_plot.pdf 73 2. output.junctionSaturation_plot.pdf
67 74
68 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/junction_saturation.png 75 .. image:: http://rseqc.sourceforge.net/_images/junction_saturation.png
76 :height: 600 px
77 :width: 600 px
78 :scale: 80 %
69 79
70 In this example, current sequencing depth is almost saturated for "known junction" (red line) detection because the number of "known junction" reaches a plateau. In other words, nearly all "known junctions" (expressed in this particular tissue) have already been detected, and continue sequencing will not detect additional "known junction" and will only increase junction coverage (i.e. junction covered by more reads). While current sequencing depth is not saturated for novel junctions (green). 80 In this example, current sequencing depth is almost saturated for "known junction" (red line) detection because the number of "known junction" reaches a plateau. In other words, nearly all "known junctions" (expressed in this particular tissue) have already been detected, and continue sequencing will not detect additional "known junction" and will only increase junction coverage (i.e. junction covered by more reads). While current sequencing depth is not saturated for novel junctions (green).
71 81
72 82
83 -----
84
85 About RSeQC
86 +++++++++++
87
88 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.
89
90 The RSeQC package is licensed under the GNU GPL v3 license.
91
92 .. image:: http://rseqc.sourceforge.net/_static/logo.png
93
94 .. _RSeQC: http://rseqc.sourceforge.net/
95
96
97
73 </help> 98 </help>
74 </tool> 99 </tool>