Mercurial > repos > nilesh > rseqc

comparison junction_annotation.xml @ 31:cc5eaa9376d8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 93c0e1cc65c6
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="junction_annotation" name="Junction Annotation"> 1 <tool id="junction_annotation" name="Junction Annotation" version="1.1">
2 <description>compares detected splice junctions to reference gene model</description> 2 <description>compares detected splice junctions 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_annotation.py -i $input -o output -r $refgene 8 <command> junction_annotation.py -i $input -o output -r $refgene
8 9
9 #if $intron.hasIntron 10 #if $intron.hasIntron
10 -m $intron.min_Intron 11 -m $intron.min_Intron
11 #end if 12 #end if
12 13
20 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" /> 21 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
21 </when> 22 </when>
22 </conditional> 23 </conditional>
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <data format="xls" name="outputxls" from_work_dir="output.junction.xls"/> 26 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
26 <data format="r" name="outputr" from_work_dir="output.junction_plot.r" /> 27 <data format="r" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
27 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf"/> 28 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
28 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" /> 29 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
29 </outputs> 30 </outputs>
31 <stdio>
32 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
33 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
34 </stdio>
30 <help> 35 <help>
31 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 36 junction_annotation.py
37 ++++++++++++++++++++++
32 38
33 ----- 39 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
40 format, this program will compare detected splice junctions to reference gene model. splicing
41 annotation is performed in two levels: splice event level and splice junction level.
34 42
35 About RSeQC 43 * splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events.
36 +++++++++++ 44 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
37 45
38 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 All detected junctions can be grouped to 3 exclusive categories:
39 47
40 The RSeQC package is licensed under the GNU GPL v3 license. 48 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site
49 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model.
50 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model
51 3. partial_novel: One of the splice site (5'SS or 3'SS) is new, while the other splice site is annotated (known)
41 52
42 Inputs 53 Inputs
43 ++++++++++++++ 54 ++++++++++++++
44 55
45 Input BAM/SAM file 56 Input BAM/SAM file
54 65
55 Output 66 Output
56 ++++++++++++++ 67 ++++++++++++++
57 68
58 1. output.junc.anno.junction.xls: 69 1. output.junc.anno.junction.xls:
59 - chrom ID 70 - chrom ID
60 - start position of junction (coordinate is 0 based) 71 - start position of junction (coordinate is 0 based)
61 - end position of junction (coordinate is 1 based) 72 - end position of junction (coordinate is 1 based)
62 - number of splice events supporting this junction 73 - number of splice events supporting this junction
63 - 'annotated', 'complete_novel' or 'partial_novel'. 74 - 'annotated', 'complete_novel' or 'partial_novel'.
64 2. output.anno.junction_plot.r: R script to generate pie chart 75 2. output.anno.junction_plot.r: R script to generate pie chart
65 3. output.splice_junction.pdf: plot of splice junctions 76 3. output.splice_junction.pdf: plot of splice junctions
66 4. output.splice_events.pdf: plot of splice events 77 4. output.splice_events.pdf: plot of splice events
67 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/junction.png 78
79 .. image:: http://rseqc.sourceforge.net/_images/junction.png
80 :height: 400 px
81 :width: 850 px
82 :scale: 80 %
83
84 -----
85
86 About RSeQC
87 +++++++++++
88
89 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.
90
91 The RSeQC package is licensed under the GNU GPL v3 license.
92
93 .. image:: http://rseqc.sourceforge.net/_static/logo.png
94
95 .. _RSeQC: http://rseqc.sourceforge.net/
68 96
69 97
70 98
71 99
72 </help> 100 </help>