Let's say I have run Homer's "annotatePeaks.pl" on multiple tissues (eye, liver, spleen), and get, lets say, X, Y, and Z total annotated genes/regions, where X, Y, and Z are just different numbers. My thought was that if I merged the peak files from these tissues (mergePeaks.pl) and run annotatePeaks.pl on that combined set, I would get X+Y+Z total annotated genes/regions, but I do not see this.
My reasoning here has to be incorrect, yet I do not know why for sure. I would appreciate any insights as to why I find this difference.
edited for readability
1 answer
Doesn't Homer mergePeaks.pl cluster peaks within 100 bp? I think this is a default operation even when you have not specified the 100 bp distance using -d. This would explain why you see fewer region in the merged annotated peak file. Can you check your merged peak file (that you generated using mergePeaks.pl) to confirm it had X+Y+Z regions ?
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