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.
•
written
by
igor
2 answers
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.
Check out these papers:
•
written
by
BioinfGuru
Log in to answer this question.
-
ATACseq: Extract Mono-nucleosome information from di- and tri-nucleosome data
written by Deep •
-
Tn5 bias in atac-seq
written by srhic •
-
Assigning nucleosome peaks to transcription factor bound locations(obtained by ChIP-seq)
written by sshibin •
-
Any tools for nucleosome phasing analysis of ATAC-Seq data?
written by srhic •
-
Can I use deeptools to calculate nucleosome positions?
written by a.rex
-
lack of replicates in single-cell RNA-seq
written by igor
-
ATAC-seq peak calling with MACS
written by igor
-
Identifying -1, NFR, +1 nucleosome arrangement around human TSS annotations
written by cbio
-
DANPOS2 with ATAC Seq data?
written by Sciurus •
-
Well Positioned Nucleosome Arrays And Active Promoter
written by chjiao3456 •
Have you tried MACS2? (ATAC-seq peak calling with MACS)
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
While you're correct, this is taken directly from the MACS2 README:
Just thought it might be worth trying out.
I think when they say nucleosome-seq, they mean something like MNase-seq where all reads are capturing the nucleosomes.