diff bamFingerprint.xml @ 5:1f312af2f8db draft

Uploaded

--- a/bamFingerprint.xml	Mon Aug 05 11:36:11 2013 -0400
+++ b/bamFingerprint.xml	Tue Aug 06 08:20:47 2013 -0400
@@ -141,15 +141,20 @@
 
 **What it does**
 
-Samples indexed bam files and plots a profile for each bam file. At each
-sample position all reads overlaping a window (bin) of specified length are
-counted. This counts are then sorted and the cumulative sum plotted
+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).
+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
+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.
 
 -----
 
 .. class:: infomark
 
-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`_.
+If you would like to give us feedback or you run into any trouble, please sent an email to [e-mail]
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.