Mercurial > repos > nilesh > rseqc

annotate junction_saturation.xml @ 41:e1dd49718284

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixed tool versions
author Lance Parsons <lparsons@princeton.edu>
date Wed, 23 Jul 2014 10:52:30 -0400
parents 1e66f05a23aa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
40
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="2.3.9">
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
2 <description>detects splice junctions from each subset and compares them to reference gene model</description>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
3 <requirements>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
4 <requirement type="package" version="3.0.1">R</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
5 <requirement type="package" version="1.7.1">numpy</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
6 <requirement type="package" version="2.3.9">rseqc</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
7 </requirements>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
8 <command> junction_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
9
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
10 #if $percentiles.specifyPercentiles
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
11 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
12 #end if
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
13
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
14 </command>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
15 <stdio>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
18 </stdio>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
19 <inputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
21 <param name="refgene" type="data" format="bed" label="reference gene model" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
22 <param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
23 <param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="1" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
24 <conditional name="percentiles">
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
25 <param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
26 <when value="true">
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
27 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
28 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
29 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
30 </when>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
31 </conditional>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
32 </inputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
33 <outputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
34 <data format="txt" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
35 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
36 </outputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
37 <help>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
38 junction_saturation.py
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
39 ++++++++++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
40
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
41 It's very important to check if current sequencing depth is deep enough to perform
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
42 alternative splicing analyses. For a well annotated organism, the number of expressed genes
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
43 in particular tissue is almost fixed so the number of splice junctions is also fixed. The fixed
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
44 splice junctions can be predetermined from reference gene model. All (annotated) splice
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
45 junctions should be rediscovered from a saturated RNA-seq data, otherwise, downstream
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
46 alternative splicing analysis is problematic because low abundance splice junctions are
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
47 missing. This module checks for saturation by resampling 5%, 10%, 15%, ..., 95% of total
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
48 alignments from BAM or SAM file, and then detects splice junctions from each subset and
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
49 compares them to reference gene model.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
50
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
51 Inputs
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
52 ++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
53
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
54 Input BAM/SAM file
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
55 Alignment file in BAM/SAM format.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
56
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
57 Reference gene model
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
58 Gene model in BED format.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
59
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
60 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5)
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
61 Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
62
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
63 Minimum intron length (default=50)
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
64 Minimum intron length (bp).
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
65
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
66 Minimum coverage (default=1)
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
67 Minimum number of supportting reads to call a junction.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
68
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
69 Output
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
70 ++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
71
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
72 1. output.junctionSaturation_plot.r: R script to generate plot
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
73 2. output.junctionSaturation_plot.pdf
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
74
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
75 .. image:: http://rseqc.sourceforge.net/_images/junction_saturation.png
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
76 :height: 600 px
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
77 :width: 600 px
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
78 :scale: 80 %
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
79
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
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).
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
81
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
82
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
83 -----
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
84
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
85 About RSeQC
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
86 +++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
87
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
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.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
89
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
90 The RSeQC package is licensed under the GNU GPL v3 license.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
91
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
92 .. image:: http://rseqc.sourceforge.net/_static/logo.png
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
93
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
94 .. _RSeQC: http://rseqc.sourceforge.net/
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
95
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
96
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
97
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
98 </help>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
99 </tool>