HOMER
Software for motif discovery and ChIP-Seq analysis
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
i.e. annotatePeaks.pl PU1peaks.txt mm8r -size 200 -center pu1.motif > pu1centeredPeaks.txt
Back to ChIP-Seq Analysis
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu