Question: FAIRE-seq peak calling ZINBA or MACS
gravatar for asharmatelome
4.7 years ago by
United States
asharmatelome60 wrote:

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?? 

ADD COMMENTlink modified 4.7 years ago by dariober11k • written 4.7 years ago by asharmatelome60

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

ADD REPLYlink written 3.6 years ago by boczniak767680
gravatar for dariober
4.7 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

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.

ADD COMMENTlink written 4.7 years ago by dariober11k
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