Closed ChunjieJiang closed 2 years ago
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.
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.
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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?