6.1 years ago by
AnnotatePeaks should be able to do this.
annotatePeaks peakfile1.bed genome -size # -hist # -noadj -d peakfile1.bed > output.txt
Here the first peak file will be the reference against which the second peak file will be plotted against.
-size # is the area around the first peak file about which you want to plot the second peak file. i.e. -size 500 would be +/-250 bp around the first peak file
-noadj option means you don't normalize the # of peaks or reads in either dataset, so the Y-axis should give you the number of peaks in each plot.
-hist# refers to the bin size
Check out the HOMER manual, under the "Histograms of Tag Directories" heading. This gives you instructions that I think will help you, straight from the author of the tool, rather than a novice, such as myself.