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shawnzhangyx / PePr

a peak-calling and differential analysis tool for replicated ChIP-Seq data
GNU General Public License v3.0
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Remove chip1 / chip2 intersecting regions #16

Open rcavalcante opened 8 years ago

rcavalcante commented 8 years ago

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 commented 8 years ago

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

On Wednesday, June 15, 2016, Raymond Cavalcante notifications@github.com 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 commented 8 years ago

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 commented 8 years ago

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