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How to use Diffbind to quantify signal in a set of custom peaks

Hi, I would like to use Diffbind to quantify signal at a custom set of regions/peaks Therefore, I would like to leave the set of peaks "untouched", avoiding the generation of consensus peaks or merging, etc. I've found several posts on this issue, and tried many things, but Im still confused and the peaks seem to be always being merged to some degree whatever I try.

Could anyone point me to the right direction on how use Diffbind in this way? Any insight will be much aporeciated.

Best wishes

atac-seq diffbind
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written by enanoide • enanoide

1 answer

I assume your custom set of peaks have overlapping or book-ended peaks like:

    |---------------------------|
              peak1
                           |----------------------------------------------------|
                                                        peak2

and this is what you mean by "merging"? Have you tried setting DBA$config$mergeOverlap to 1e9?

• 0 views • link
written by LChart LChart

Thanks for the answer. I have tried to do dba twice, the second after setting that option to a number larger than the peak. It does not seem to work. Ill try with 1e9, thanks. I should do the dba twice, right?

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written by enanoide • enanoide

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