nucleosome positioning using ATAC-seq

Question

[igor]

Are there any tools for nucleosome positioning using ATAC-seq data? I am aware of NucleoATAC, but that is the only I found.

The original ATAC-seq paper used Danpos, which is designed for MNase-seq, and they even mention it may not be ideal. That may not be a good alternative.

[Sinji]

Have you tried MACS2? (ATAC-seq peak calling with MACS)

[igor]

MACS is for peak calling. For ATAC-seq, that would be open chromatin. Nucleosome positioning is something else.

Figure 1 here is helpful: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/1756-8935-7-33

[Sinji]

While you're correct, this is taken directly from the MACS2 README:

1. For certain nucleosome-seq data, we need to pileup the centers of nucleosomes using a half-nucleosome size for wavelet analysis (e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about 147bps, this option can be used: '--nomodel --shift 37 --extsize 73'.

Just thought it might be worth trying out.

[igor]

I think when they say nucleosome-seq, they mean something like MNase-seq where all reads are capturing the nucleosomes.

Answer 1

[ejm32]

There are a number of packages in bioconductor aimed at nucleosome positioning (PING, nucleR, NuPOP). Most are designed with MNase in mind, but I wouldn't think that would matter especially if you are only giving the algorithms the mono-nuclesome DNA. A post-doc next door was using iNPS (http://www.nature.com/articles/ncomms5909) with some good success. Also check out this paper on cell-free DNA. I think there method is easily adaptable to ATAC data.

Answer 2

[BioinfGuru]

Check out these papers:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309995/

https://academic.oup.com/bib/article/17/5/745/2262046/Nucleosome-positioning-resources-and-tools-online