Question: should I use only nucleosome free region as ATACseq input?

Question

Question: should I use only nucleosome free region as ATACseq input?

ftucos opened this issue 2 years ago · 2 comments

Hi, I was wondering if filtering the ATACseq bam file used as input for PECA2 to retain only Nucleosome Free Regions is required and or would increase the accuracy of the analysis.

Answer 1 · 2022-10-05T18:52:43.000Z

Interesting question, we never tried this before. My guess is that using whole bam file is better because a local normalization is used in PECA.

Answer 2 · 2022-10-05T19:36:52.000Z

Thank you very much for your feedback.
Maybe I'll try both and I'll let you know if I observe relevant differences.