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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 8dbd613bd835
children 580ee0c4bc4e
comparison
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30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="infer_experiment" name="Infer Experiment"> 1 <tool id="infer_experiment" name="Infer Experiment" version="1.1">
2 <description>speculates how RNA-seq were configured</description> 2 <description>speculates how RNA-seq were configured</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement>
4 <requirement type="package" version="2.3.7">rseqc</requirement> 5 <requirement type="package" version="2.3.7">rseqc</requirement>
5 </requirements> 6 </requirements>
6 <command interpreter="python"> infer_experiment.py -i $input -r $refgene 7 <command> infer_experiment.py -i $input -r $refgene
7 8
8 #if $sample_size.boolean 9 #if $sample_size.boolean
9 -s $sample_size.size 10 -s $sample_size.size
10 #end if 11 #end if
11 12
22 </conditional> 23 </conditional>
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <data format="txt" name="output" /> 26 <data format="txt" name="output" />
26 </outputs> 27 </outputs>
28 <stdio>
29 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
30 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
31 </stdio>
27 <help> 32 <help>
28 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 33 infer_experiment.py
34 +++++++++++++++++++
29 35
30 ----- 36 This program is used to speculate how RNA-seq sequencing were configured, especially how
37 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
38 information to the underneath gene model.
31 39
32 About RSeQC
33 +++++++++++
34
35 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.
36
37 The RSeQC package is licensed under the GNU GPL v3 license.
38 40
39 Inputs 41 Inputs
40 ++++++++++++++ 42 ++++++++++++++
41 43
42 Input BAM/SAM file 44 Input BAM/SAM file
46 Gene model in BED format. 48 Gene model in BED format.
47 49
48 Number of usable sampled reads (default=200000) 50 Number of usable sampled reads (default=200000)
49 Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower. 51 Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower.
50 52
53 Outputs
54 +++++++
51 55
52 Output 56 For pair-end RNA-seq, there are two different
53 ++++++++++++++ 57 ways to strand reads (such as Illumina ScriptSeq protocol):
54 This program is used to speculate how RNA-seq sequencing were configured, especially how reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping information to the underneath gene model. Generally, strand specific RNA-seq data should be handled differently in both visualization and RPKM calculation.
55 58
56 For pair-end RNA-seq, there are two different ways to strand reads: 59 1. 1++,1--,2+-,2-+
57 60
58 1) 1++,1--,2+-,2-+ 61 * read1 mapped to '+' strand indicates parental gene on '+' strand
59 - read1 mapped to '+' strand indicates parental gene on '+' strand 62 * read1 mapped to '-' strand indicates parental gene on '-' strand
60 - read1 mapped to '-' strand indicates parental gene on '-' strand 63 * read2 mapped to '+' strand indicates parental gene on '-' strand
61 - read2 mapped to '+' strand indicates parental gene on '-' strand 64 * read2 mapped to '-' strand indicates parental gene on '+' strand
62 - read2 mapped to '-' strand indicates parental gene on '+' strand 65
63 2) 1+-,1-+,2++,2-- 66 2. 1+-,1-+,2++,2--
64 - read1 mapped to '+' strand indicates parental gene on '-' strand 67
65 - read1 mapped to '-' strand indicates parental gene on '+' strand 68 * read1 mapped to '+' strand indicates parental gene on '-' strand
66 - read2 mapped to '+' strand indicates parental gene on '+' strand 69 * read1 mapped to '-' strand indicates parental gene on '+' strand
67 - read2 mapped to '-' strand indicates parental gene on '-' strand 70 * read2 mapped to '+' strand indicates parental gene on '+' strand
71 * read2 mapped to '-' strand indicates parental gene on '-' strand
68 72
69 For single-end RNA-seq, there are also two different ways to strand reads: 73 For single-end RNA-seq, there are also two different ways to strand reads:
70 74
71 1) ++,-- 75 1. ++,--
72 -read mapped to '+' strand indicates parental gene on '+' strand 76
73 - read mapped to '-' strand indicates parental gene on '-' strand 77 * read mapped to '+' strand indicates parental gene on '+' strand
74 2) +-,-+ 78 * read mapped to '-' strand indicates parental gene on '-' strand
75 - read mapped to '+' strand indicates parental gene on '-' strand 79
76 - read mapped to '-' strand indicates parental gene on '+' strand 80 2. +-,-+
81
82 * read mapped to '+' strand indicates parental gene on '-' strand
83 * read mapped to '-' strand indicates parental gene on '+' strand
84
77 85
78 Example Output 86 Example Output
79 ++++++++++++++ 87 ++++++++++++++
80 88
81 **Example1** :: 89 **Example1** ::
111 Fraction of reads explained by "+-,-+": 0.0160 119 Fraction of reads explained by "+-,-+": 0.0160
112 Fraction of reads explained by other combinations: 0.0000 120 Fraction of reads explained by other combinations: 0.0000
113 ========================================================= 121 =========================================================
114 122
115 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene. 123 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
124
125
126 -----
127
128 About RSeQC
129 +++++++++++
130
131 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.
132
133 The RSeQC package is licensed under the GNU GPL v3 license.
134
135 .. image:: http://rseqc.sourceforge.net/_static/logo.png
136
137 .. _RSeQC: http://rseqc.sourceforge.net/
138
139
116 </help> 140 </help>
117 </tool> 141 </tool>