macs and bedtools

Question

[marina-orlova]

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?

Answer 1

[Ming Tommy Tang]

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