Remove chip1 / chip2 intersecting regions

[rcavalcante]

I've observed that chip1 peaks and chip2 peaks can overlap a little bit at the edges. We've discussed how that comes from the windowing approach, but would it be possible to add a post-processing step that removes the regions that are in the intersection of chip1 and chip2 peaks from both of the results files?

[shawnzhangyx]

Hi Ray, could you send me an example of it so I know what it is like?

On Wednesday, June 15, 2016, Raymond Cavalcante [email protected] wrote:

I've observed that chip1 peaks and chip2 peaks can overlap a little bit at the edges. We've discussed how that comes from the windowing approach, but would it be possible to add a post-processing step that removes the regions that are in the intersection of chip1 and chip2 peaks from both of the results files?

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[rcavalcante]

Hey Yanxiao,

I attached a zip of chip1 and chip2 peaks, plus the result of bedtools intersect -wa -wb -a chip1 -b chip2.

peak_overlaps.zip

[shawnzhangyx]

I find the easiest way is to use bedtools subtract -a chip1 -b chip2 to trim the edges.