Question about using DANPOS for histone modification comparison

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Medha Pandey

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Jul 15, 2025, 5:46:43 PMJul 15

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Hi all,

I hope you're doing well. I’m reaching out to ask if anyone has experience using the DANPOS dpos function to analyze nucleosome positioning for different histone modification marks.

Specifically, I’m curious whether the dpos method—typically used to compare nucleosome positions between samples (e.g., python danpos.py dpos sampleA:sampleB.bed.gz)—can also be applied to compare datasets from different histone marks, such as H3K4me3 vs. H3K27ac. I understand that DANPOS is designed with MNase-seq data in mind, but I’m wondering if this method is also suitable for cfChIP-seq or similar ChIP-seq-based datasets targeting histone modifications.

Any insights, suggestions, or experiences would be greatly appreciated.

Thanks in advance!

Best regards,
Medha

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