Question: Is it possible to change how DiffBind merge peaks?
0
gravatar for zhenfeng.liu1
3 months 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 • 79 views
ADD COMMENTlink modified 9 weeks ago by Rory Stark3.0k • written 3 months ago by zhenfeng.liu110
Answer: Is it possible to change how DiffBind merge peaks?
0
gravatar for Rory Stark
9 weeks ago by
Rory Stark3.0k
CRUK, Cambridge, UK
Rory Stark3.0k 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 9 weeks ago • written 9 weeks ago by Rory Stark3.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 220 users visited in the last hour