Mercurial > repos > bgruening > deeptools

comparison bamFingerprint.xml @ 5:1f312af2f8db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 06 Aug 2013 08:20:47 -0400
parents 21d563d5f2b2
children c5847db0cb41
comparison
equal deleted inserted replaced
4:c8a0dc481493 5:1f312af2f8db
139 </outputs> 139 </outputs>
140 <help> 140 <help>
141 141
142 **What it does** 142 **What it does**
143 143
144 Samples indexed bam files and plots a profile for each bam file. At each 144 This tool is based on a method developed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3).
145 sample position all reads overlaping a window (bin) of specified length are 145 The resulting plot can be used to assess the strength of a ChIP (for factors that bind to narrow regions).
146 counted. This counts are then sorted and the cumulative sum plotted 146 The tool first samples indexed bam files and counts all reads overlapping a window (bin) of specified length.
147 These counts are then sorted according to their rank and the cumulative sum of read counts are plotted. An ideal input
148 with perfect uniform distribution of reads along the genome (i.e. without enrichments in open chromatin etc.) should
149 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
150 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
151 few bins which corresponds to high, narrow enrichments seen for transcription factors.
147 152
148 ----- 153 -----
149 154
150 .. class:: infomark 155 .. class:: infomark
151 156
152 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_. 157 If you would like to give us feedback or you run into any trouble, please sent an email to deeptools@googlegroups.com
153 158
154 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 159 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
155 160
156 161
157 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 162 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/