Question: macs and bedtools
gravatar for marina-orlova
5.6 years ago by
Russian Federation
marina-orlova70 wrote:


I have MACS2 output and now looking for peaks which are situated in introns. I have bed file with introns from USCS for my species. What file with peaks should I use for bedtools intersection? Peaks summit (.bed) or narrow peak (.bed), both from MACS2 output?

peaks macs bedtools • 2.8k views
ADD COMMENTlink modified 5.6 years ago by Ming Tang2.5k • written 5.6 years ago by marina-orlova70
gravatar for Ming Tang
5.6 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

Use narrow peaks. Summit file contains the higest coverage point inside the peak.

ADD COMMENTlink written 5.6 years ago by Ming Tang2.5k
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