Software for motif discovery and ChIP-Seq analysis

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ChIP-Seq Analysis: Centering Peaks on Motifs

One cool analysis strategy is to center peaks on a specific motif.  For example, by centering peak for the ETS Transcription Factor PU.1 on the PU.1 motif (GAGGAAGT), you can map the spacial relationship between the bound PU.1 motif and other sequence features and ChIP-Seq tags.

To center peaks on a motif, run annotatePeaks.pl with the following options:

annotatePeaks.pl <peak file> <genome> -size <#> -center <motif file> > newpeakfile.txt

i.e. annotatePeaks.pl PU1peaks.txt mm8r -size 200 -center pu1.motif > pu1centeredPeaks.txt


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