macs and bedtools

Hello

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?

bedtools macs peaks

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updated 12.1 years ago by Ming Tommy Tang

• written 12.1 years ago by marina-orlova

1 answer

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

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written 12.1 years ago by Ming Tommy Tang

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