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ay-lab / FitHiChIP

Statistically Significant loops from HiChIP data
MIT License
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CHIP-seq inferred from HICHIP peak #69

Closed xumai-du closed 2 years ago

xumai-du commented 2 years ago

If we use PeakInferHiChIP.sh to infer the ChIP-seq peak from HIChIP data, we got .narrowPeak formatted peak file. Is it OK for Histone HICHIP as .broadPeak formatted peak files are normally used for many other applications? Thanks!

ay-lab commented 2 years ago

Hi @xumai-du We recommend using narrow peak formatted files, since broad peaks are often much wide, and span a much higher region from the summits. Therefore, using narrow peak files would better indicate the protein enriched regions.