Mercurial > repos > bgruening > deeptools_plot_fingerprint

comparison plotFingerprint.xml @ 1:a6d0ddc266bf draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:26:21 -0500
parents c1b46e0cb7ca
children 91b340ca9e92
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0:c1b46e0cb7ca 1:a6d0ddc266bf
111 </tests> 111 </tests>
112 <help> 112 <help>
113 <![CDATA[ 113 <![CDATA[
114 114
115 115
116 **What it does** 116 What it does
117 ---------------
117 118
118 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background) 119 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
119 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). 120 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
121
122
123 Output
124 ---------
125
126 The default output is a diagnostic plot (see below for an example and further down for some background information).
127
128 Optionally, you can obtain the table of raw counts that was used to generate the plot.
129
130 .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
131 :width: 600
132 :height: 395
133
134
135 Example plot
136 -------------
137
138 What follows is the output of ``plotFingerprint`` with our test ChIP-Seq data sets, limiting the analysis to chromosome X. Single-end reads were extended to
139 200 bp (advanced options).
140
141 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
142 :width: 600
143 :height: 450
144
145 -----------------------------
146
147 Background
148 --------------
120 149
121 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length. 150 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length.
122 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) 151 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
123 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments 152 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments
124 result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion 153 result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
125 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are 154 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
126 most commonly seen with transcription factors. 155 most commonly seen with transcription factors.
127 156
128 157
129 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png 158 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
130 159 :width: 600
131 160 :height: 294
132 You can find more details on the plotFingerprint doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotFingerprint.html
133
134
135 **Output files**:
136
137 - Diagnostic plot
138 - (optional) Data matrix of raw counts
139
140 **Output with test dataset**:
141
142 What follows is the output of plotFingerprint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
143 200 bp (advanced options).
144
145 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
146
147 161
148 ----- 162 -----
149 163
150 @REFERENCES@ 164 @REFERENCES@
151 ]]> 165 ]]>