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comparison genetrack.xml @ 12:cd105fdfb0da draft

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author greg
date Wed, 16 Dec 2015 12:22:27 -0500
parents 497e3274f70b
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11:497e3274f70b 12:cd105fdfb0da
36 <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" /> 36 <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" />
37 </when> 37 </when>
38 </conditional> 38 </conditional>
39 <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." /> 39 <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
40 <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." /> 40 <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
41 <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" /> 41 <param name="up_width" type="integer" value="10" min="0" label="Exclusion zone of upstream called peaks" />
42 <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" /> 42 <param name="down_width" type="integer" value="10" min="0" label="Exclusion zone of downstream called peaks" />
43 <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." /> 43 <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
44 </inputs> 44 </inputs>
45 <outputs> 45 <outputs>
46 <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}"> 46 <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
47 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" /> 47 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
86 </test> 86 </test>
87 </tests> 87 </tests>
88 <help> 88 <help>
89 **What it does** 89 **What it does**
90 90
91 Genetrack supports ChIP experiments. The peak caller takes a standard set of data on both the sense and 91 <![CDATA[
92 antisense strands (ScIdx format) and smooths their relative reads. It then predicts the peaks present in 92
93 the smoothed dataset and uses those peak locations to find the maximal non-overlapping subset. It then 93 GeneTrack separately identifies peaks on the forward "+” and reverse “-” strand. The way that GeneTrack works
94 selects the highest peak and establishes an exclusion zone, and no other predicted peaks will be reported 94 is to replace each tag with a probabilistic distribution of occurrences for that tag at and around its mapped
95 within the exclusion zone. Finally, it ensures each peak is above a threshold and that two peaks are not 95 genomic coordinate. The distance decay of the probabilistic distribution is set by adjusting the value of the
96 too close to each other. 96 tool's **Sigma to use when smoothing reads** parameter. GeneTrack then sums the distribution over all mapped
97 tags. This results in a smooth continuous trace that can be globally broadened or tightened by adjusting the
98 sigma value. GeneTrack starts with the highest smoothed peak first, treating each strand separately if indicated
99 by the data, then sets up an exclusion zone (centered over the peak) defined by the value of the **Peak exclusion
100 zone** parameter (see figure). The exclusion zone prevents any secondary peaks from being called on the same strand
101 within that exclusion zone. In rare cases, it may be desirable to set different exclusion zones upstream (more 5’)
102 versus downstream (more 3’) of the peak.
103
104 ]]>
105
106 .. image:: $PATH_TO_IMAGES/genetrack.png
97 107
98 ----- 108 -----
99 109
100 **Options** 110 **Options**
101 111
102 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks. 112 * **Sigma to use when smoothing reads** - Smooths clusters of tags via a Gaussian distribution.
103 * **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called. 113 * **Peak exclusion zone** - Exclusion zone around each peak, eliminating all other peaks on the same strand that are within a ± bp distance of the peak.
104 * **Upstream width of called peaks** - Upstream width of called peaks. 114 * **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
105 * **Downstream width of called peaks** - Downstream width of called peaks. 115 * **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
106 * **Filter** - Absolute read filter. Restricts output to only peaks with larger peak height. 116 * **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
107 </help> 117 </help>
108 <expand macro="citations" /> 118 <expand macro="citations" />
109 </tool> 119 </tool>