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LiuLabUB / HMMRATAC

HMMRATAC peak caller for ATAC-seq data
GNU General Public License v3.0
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What is the major difference between MACS and HMMRATAC? #5

Closed hmyh1202 closed 6 years ago

hmyh1202 commented 6 years ago

Hi， what is the difference betwwen MACS2 and HMMRATAC in peak calling when input ATAC-seq data,

and the difference in detecting chrom stat when using iNPS and HMMRATAC ?

EvanTarbell commented 6 years ago

The HMMRATAC algorithm, and its advantages over MACS2 (as well as F-seq and Hotspot2), are described in: https://www.biorxiv.org/content/early/2018/04/24/306621

EvanTarbell commented 6 years ago

Briefly, we observed a distinct pattern of short and long sequence fragments, generated by ATAC-seq, at known accessible elements. HMMRATAC uses a HMM to model that pattern to identify accessible regions genome-wide. MACS2 uses a local poisson distribution and only considers the number of fragments, regardless of size, at a potential accessible element.

EvanTarbell commented 6 years ago

@hmyh1202 I am currently in the process of publishing the manuscript for this code and wanted to have some user feedback for the reviewers. I would like to ask you a few questions. 1) What type of machine did you run HMMRATAC on? 2) How easy was it for you to run the algorithm? 3) How well have I been in addressing your concerns about using HMMRATAC? Thank you!