Question: nucleosome positioning using ATAC-seq
1
gravatar for igor
23 months ago by
igor7.1k
United States
igor7.1k wrote:

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.

atac-seq nucleosome • 2.1k views
ADD COMMENTlink modified 20 months ago by YaGalbi1.4k • written 23 months ago by igor7.1k

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

ADD REPLYlink written 23 months ago by Sinji2.7k
1

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

ADD REPLYlink written 23 months ago by igor7.1k
1

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.

ADD REPLYlink written 23 months ago by Sinji2.7k

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

ADD REPLYlink written 23 months ago by igor7.1k
2
gravatar for ejm32
23 months ago by
ejm32420
Boston, MA
ejm32420 wrote:

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.

ADD COMMENTlink written 23 months ago by ejm32420
0
gravatar for YaGalbi
20 months ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

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

ADD COMMENTlink modified 18 months ago by h.mon22k • written 20 months ago by YaGalbi1.4k
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