How to retrieve peak summit from DiffBind peaks
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fbleao • 0
@7a40ce29
Last seen 3 days ago
United States

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

DiffBind • 92 views
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Rory Stark ★ 3.9k
@rory-stark-5741
Last seen 19 minutes ago
CRUK, Cambridge, UK

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)
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