Question: Is it possible to change how DiffBind merge peaks?
0
gravatar for zhenfeng.liu1
4 weeks ago by
zhenfeng.liu110 wrote:

The default behavior of DiffBind when merging peaks from different samples is that peaks with at least 1 bp overlap will be merged. For example, peak chr1:100-300 will be merged with peak chr1:299-500. Is it possible to change this behavior, for example, requiring at least 50% bp overlap between the two peaks, so the above example won't merge? If anyone knows how to do this in DiffBind or ways using other R packages that would still be compatible with other parts of DiffBind, that would be great.

Thank you.

chipseq diffbind • 50 views
ADD COMMENTlink modified 13 days ago by Rory Stark2.8k • written 4 weeks ago by zhenfeng.liu110
Answer: Is it possible to change how DiffBind merge peaks?
0
gravatar for Rory Stark
13 days ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k wrote:

We are looking at exposing this feature in DiffBind, but currently there is no way to override the 1bp overlap.

If you are able to separately derive a merged consensus set using alternative criteria, not that you can pass it in to dba.count() and that set will be used for all the subsequent steps (so long as the intervals you pass in are not themselves overlapping).

ADD COMMENTlink modified 13 days ago • written 13 days ago by Rory Stark2.8k
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