Software for motif discovery and ChIP-Seq analysis

This is the old version of the documentation: New Version

ChIP-Seq Analysis: Finding Overlapping and Differentially Bound Peaks

HOMER provides a utility for comparing sets of peaks called mergePeaks (replacing mergePeaks.pl in v2.4).  It's default behavior is to take two or more peak files and return a single peak file containing the unique peak positions from the original files.  For example:

mergePeaks -d <maximum distance to merge> <peak file1> <peak file2> [peak file3] ... > newPeakFile.txt
The program will output a new peak file containing the merged peaks to stdout.  Peaks within the distance in bp specified by "-d <#>" will be reported as the weighted average position (based on 6th column peak scores) between the peaks found within the common region (default=100 bp).  The origin of the peaks is specified in the 7th column of the new peak file.  Alternatively you can specify "-d given" to require a specific overlap between the start and end coordinates of the peaks.  This is more useful if comparing large regions as opposed to peaks, which tend to be highly localized.  The program will also output the numbers for creating a venn diagram, and these can be directed to a specific file by specifying "-venn <filename>".

Merging peaks together into a single file is very useful for certain types of analysis, such as making scatter plots that compare the tag-densities between peaks from separate experiments - in this case you want to count tags at specific and common regions.  Alternatively, you may be interested in separating the peaks into common and specific sets for focused analysis.  To do this use the "-prefix <filename>" option - this will create separate files based on overlapping peaks for each set of peaks. For example:

mergePeaks -d 100 pu1.peaks cebp.peaks -prefix mmm

This will create files named "mmm_pu1.peaks", "mmm_cebp.peaks", and "mmm_pu1.peaks_cebp.peaks".

Peak Co-Occurance Statistics

The mergePeaks program will also find calculate the statistics of co-occurence between peaks in a pairwise fashion. 

Differentially Bound Peaks

For now, simply use peak finding to find peaks that are differentially enriched between two samples.  Simply substitute the "Tag Directory" of the Input experiment with that of another experiment.

Back to ChIP-Seq Analysis

Can't figure something out? Questions, comments, concerns, or other feedback: