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comparison junction_annotation.xml @ 43:378d05d35705 draft

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author lparsons
date Wed, 23 Jul 2014 10:58:28 -0400
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1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="2.3.9">
2 <description>compares detected splice junctions to reference gene model</description>
3 <requirements>
4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.9">rseqc</requirement>
7 </requirements>
8 <command>
9 junction_annotation.py
10 -i $input -o output -r $refgene
11 #if $intron.hasIntron
12 -m $intron.min_Intron
13 #end if
14 </command>
15 <stdio>
16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
18 </stdio>
19 <inputs>
20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
21 <param name="refgene" type="data" format="bed" label="reference gene model" />
22 <conditional name="intron">
23 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
24 <when value="true">
25 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
31 <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
32 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
33 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
34 </outputs>
35 <help>
36 junction_annotation.py
37 ++++++++++++++++++++++
38
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.
42
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.
44 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
45
46 All detected junctions can be grouped to 3 exclusive categories:
47
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)
52
53 Inputs
54 ++++++++++++++
55
56 Input BAM/SAM file
57 Alignment file in BAM/SAM format.
58
59 Reference gene model
60 Gene model in BED format.
61
62 Minimum intron length (default=50)
63 Minimum intron length (bp).
64
65
66 Output
67 ++++++++++++++
68
69 1. output.junc.anno.junction.xls:
70 - chrom ID
71 - start position of junction (coordinate is 0 based)
72 - end position of junction (coordinate is 1 based)
73 - number of splice events supporting this junction
74 - 'annotated', 'complete_novel' or 'partial_novel'.
75 2. output.anno.junction_plot.r: R script to generate pie chart
76 3. output.splice_junction.pdf: plot of splice junctions
77 4. output.splice_events.pdf: plot of splice events
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/
96
97
98
99
100 </help>
101 </tool>