I got one question in terms of how to filter reads except for nucleosome free regions.
As you can see on your website, there is one step to filter out high nucleosome signals.
Then there is no step for extracting nucleosome free regions.
Given bulk ATAC-seq analysis, it's highly recommended to focus on nucleosome free regions.
I just wonder whether it's technically impossible or is there any built-in tools to capture only nucleosome free regions in this package?
Furthermore, is it okay to analyze scATAC-seq data with reads containing nucleosomes?
Dear.Signac developers
I got one question in terms of how to filter reads except for nucleosome free regions. As you can see on your website, there is one step to filter out high nucleosome signals.
https://stuartlab.org/signac/articles/pbmc_vignette
Then there is no step for extracting nucleosome free regions. Given bulk ATAC-seq analysis, it's highly recommended to focus on nucleosome free regions.
I just wonder whether it's technically impossible or is there any built-in tools to capture only nucleosome free regions in this package? Furthermore, is it okay to analyze scATAC-seq data with reads containing nucleosomes?
Best Regards.