About ATAC-seq peakcalling

[ChunjieJiang]

Hi

Genrich is a wonderful tool for ATAC-seq data. I have used it in my cell metabolism paper (DOI: 10.1016/j.cmet.2021.06.004). And I'll used it again in my new project.

I have one question about the peak calling. I was told by other senior analyzer that only nucleosome-free (NFR) reads should be considered for peak calling. Does Genrich containing steps to remove Mono nucleosome reads and Nucleosome reads, and do peak calling only using nucleosome-free (NFR) reads?

[jsh58]

Thanks for the question. There is no option in Genrich to filter fragments based on size. While it is true that ATAC-seq fragments follow a characteristic size distribution, it is not the case that all fragments above a certain size (~150bp) are derived from DNA segments surrounding one or more nucleosomes. I do not know of a method to separate reads derived from longer fragments into those that surrounded nucleosomes versus those that did not.

[ChunjieJiang]

Hi John, Thanks for your reply. Best wishes, Chunjie

…

On Sun, Nov 28, 2021 at 6:44 PM John M. Gaspar ***@***.***> wrote: Thanks for the question. There is no option in Genrich to filter fragments based on size. While it is true that ATAC-seq fragments follow a characteristic size distribution, it is *not* the case that *all* fragments above a certain size (~150bp) are derived from DNA segments surrounding one or more nucleosomes. I do not know of a method to separate reads derived from longer fragments into those that surrounded nucleosomes versus those that did not. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#84 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKCDAKA7KFKILUUTOKGDAJDUOLEF5ANCNFSM5IR5YK2Q> .