Mercurial > repos > bgruening > deeptools
diff bamFingerprint.xml @ 24:d7c9fd76e41e draft
Uploaded
author | bgruening |
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date | Tue, 04 Feb 2014 09:12:07 -0500 |
parents | 8c452f37c896 |
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--- a/bamFingerprint.xml Tue Feb 04 03:38:20 2014 -0500 +++ b/bamFingerprint.xml Tue Feb 04 09:12:07 2014 -0500 @@ -120,11 +120,13 @@ **What it does** -This tool is based on a method developed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). -The resulting plot can be used to assess the strength of a ChIP (for factors that bind to narrow regions). +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) +and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). + The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length. -These counts are then sorted according to their rank and the cumulative sum of read counts are plotted. An ideal input -with perfect uniform distribution of reads along the genome (i.e. without enrichments in open chromatin etc.) should +These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) +and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads +along the genome (i.e. without enrichments in open chromatin etc.) should generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in few bins which corresponds to high, narrow enrichments seen for transcription factors. @@ -133,9 +135,7 @@ .. image:: $PATH_TO_IMAGES/QC_fingerprint.png -You can find more details in the `bamFingerprint wiki`_. - -.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint +You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint **Output files**: