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comparison bamFingerprint.xml @ 24:d7c9fd76e41e draft

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author bgruening
date Tue, 04 Feb 2014 09:12:07 -0500
parents 8c452f37c896
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23:8c452f37c896 24:d7c9fd76e41e
118 </outputs> 118 </outputs>
119 <help> 119 <help>
120 120
121 **What it does** 121 **What it does**
122 122
123 This tool is based on a method developed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). 123 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
124 The resulting plot can be used to assess the strength of a ChIP (for factors that bind to narrow regions). 124 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
125
125 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length. 126 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
126 These counts are then sorted according to their rank and the cumulative sum of read counts are plotted. An ideal input 127 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
127 with perfect uniform distribution of reads along the genome (i.e. without enrichments in open chromatin etc.) should 128 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
129 along the genome (i.e. without enrichments in open chromatin etc.) should
128 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep 130 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
129 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in 131 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
130 few bins which corresponds to high, narrow enrichments seen for transcription factors. 132 few bins which corresponds to high, narrow enrichments seen for transcription factors.
131 133
132 134
133 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png 135 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
134 136
135 137
136 You can find more details in the `bamFingerprint wiki`_. 138 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
137
138 .. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
139 139
140 140
141 **Output files**: 141 **Output files**:
142 142
143 - Diagnostic plot 143 - Diagnostic plot