Hi,

I don't have experience with R, so I ran Diffbind using Galaxy. I didn't specify the Summit option, so all my peaks have a different width.

Now I want to get the summits of the differential peaks to run motif analysis. Is there an easy way to do this from the Diffbind output files?

Thank you

You can get the summits for your consensus set by running dba.count() again with summits=TRUE, and retrieving a GRanges object with the summit position indicated for each sample:

myDBA <- dba.count(myDBA, summits=TRUE, score=DBA_SCORE_SUMMITS_POS)
summits <- dba.peakset(myDBA, bRetrieve=TRUE)