Can I use HOMER called peaks in DiffBind without making any changes to the peaks file (HOMER output file)?
You can use the pos2bed.pl utility that comes with HOMER. There is a discussion of this here:
DiffBind: reading in peaksets generated by Homer2
See particularly Gord's answer near the top.
P.S. We still have an "add support for HOMER peak format" feature in our list of to-do, maybe someday soon?
Note also that in "factor" mode, HOMER produces fixed-width peaks. For very strong peaks, that may mean that most of the reads are outside the range of the called peak (e.g. it gives you 200bp wide peaks, but the bulk of reads in a very strong peak might be more than 100bp from the centre). If you're looking at differential binding, this can give misleading results, since reads that are off the edge of the called peaks won't be counted.
Thanks a lot!
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