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comparison mmquant.xml @ 2:fc9d40c697e8 draft

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author m-zytnicki
date Tue, 11 Apr 2017 11:26:53 -0400
parents 87c5fa8651c1
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1:87c5fa8651c1 2:fc9d40c697e8
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
7 </stdio> 7 </stdio>
8 <command><![CDATA[ 8 <command><![CDATA[
9 mmquant 9 mmquant_static
10 -a "$annotation" 10 -a "$annotation"
11 -r 11 -r
12 #for $r in $reads_info 12 #for $r in $reads_info
13 ${r.reads.file_name} 13 ${r.reads.file_name}
14 #end for 14 #end for
17 ${r.reads.ext} 17 ${r.reads.ext}
18 #end for 18 #end for
19 -s 19 -s
20 #for $r in $reads_info 20 #for $r in $reads_info
21 ${r.strand} 21 ${r.strand}
22 #end for
23 -t
24 #for $r in $reads_info
25 ${r.sorted}
22 #end for 26 #end for
23 -n 27 -n
24 #for $r in $reads_info 28 #for $r in $reads_info
25 ${r.name} 29 ${r.name}
26 #end for 30 #end for
41 <option value="U" selected="yes">unknown</option> 45 <option value="U" selected="yes">unknown</option>
42 <option value="FR">forward-reverse (for paired-end reads)</option> 46 <option value="FR">forward-reverse (for paired-end reads)</option>
43 <option value="RF">reverse-forward (for paired-end reads)</option> 47 <option value="RF">reverse-forward (for paired-end reads)</option>
44 <option value="F">forward (for single-end reads)</option> 48 <option value="F">forward (for single-end reads)</option>
45 <option value="R">reverse (for single-end reads)</option> 49 <option value="R">reverse (for single-end reads)</option>
50 </param>
51 <param name="sorted" type="select" label="Sorted" multiple="false" >
52 <option value="Y" selected="yes">yes</option>
53 <option value="N">no</option>
46 </param> 54 </param>
47 </repeat> 55 </repeat>
48 <param name="overlap" type="float" value="-1" label="Overlap type" help="&lt;0: read is included, &lt;1: overlap, otherwise: # nt" /> 56 <param name="overlap" type="float" value="-1" label="Overlap type" help="&lt;0: read is included, &lt;1: overlap, otherwise: # nt" />
49 <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" /> 57 <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" />
50 <param name="count" type="integer" value="0" min="0" label="Count threshold" help="Do not display genes with less than N reads" /> 58 <param name="count" type="integer" value="0" min="0" label="Count threshold" help="Do not display genes with less than N reads" />
76 84
77 Recently, an article_ showed that RNA-Seq quantification tools are not accurate, leading to errors while finding differentially expressed genes. The authors suggest this method, that may not provide the genes that are differentially expressed (something that RNA-Seq alone cannot do), but the groups of genes that are differentially expressed. 85 Recently, an article_ showed that RNA-Seq quantification tools are not accurate, leading to errors while finding differentially expressed genes. The authors suggest this method, that may not provide the genes that are differentially expressed (something that RNA-Seq alone cannot do), but the groups of genes that are differentially expressed.
78 86
79 .. _article: http://www.genomebiology.com/2015/16/1/177 87 .. _article: http://www.genomebiology.com/2015/16/1/177
80 88
81 **Strands**
82
83 Strands can be:
84
85 * for paired-end reads: ``U`` (unknown), ``FR`` (forward-reverse), ``RF`` (reverse-forward), ``FF`` (forward-forward);
86
87 * for single-end reads: ``U`` (unknown), ``F`` (forward), ``R`` (reverse);
88
89 * Default: ``U``.
90
91 89
92 **Annotation file** 90 **Annotation file**
93 91
94 The annotation file should be in GTF. GFF might work too. The tool only uses the gene/transcript/exon types. 92 The annotation file should be in GTF. GFF might work too. The tool only uses the gene/transcript/exon types.
95 93