Question

FAIRE-seq peak calling ZINBA or MACS

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9.5 years ago

asharmatelome ▴ 60

Hi, I recently did a FAIRE-seq and did MACS peak calling using galaxy.

I was reading the original paper and apparently MACS is not the tool for FAIRE-seq peak calling..

Any experiences?

ZINBA ChIP-Seq MACS FAIRE-seq next-gen • 3.8k views

ADD COMMENT • link updated 21 months ago by Ram 44k • written 9.5 years ago by asharmatelome ▴ 60

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I've read that MACS2 are suitable for this type of data, but haven't checked it yet by myself. As cited here

ADD REPLY • link 8.3 years ago by boczniak767 ▴ 870

Ram · Answer 1 · 2015-05-07

My 2p: My impression is that the typical peaks from FAIRE are too weak to be picked up by macs, so I agree macs is not ideal in this case. I got good results with fseq. "Good results" meaning the number of peaks was more or less as expected from the literature (tens or 100s of thousands, corresponding to ~1% of the genome) and from visual inspection the peaks looked ok. The method fseq implements seems reasonable and not overly complicated. Also, fseq runs ok without much tweaking of the parameters and without a huge amount of resources. In contrast, I couldn't get zinba to complete my analyses due to memory or time constraints or other problems with the underlying algorithm, but that could be me doing the wrong things.

I know, a lot of hand waving here. In general, I find peak calling to be very unstable. Depending on the peak caller you use or the exact parameters you get widely different results.