Peak calling with nucleosomal free reads

[Y-ogativity]

Hi,

Thank you for developing and maintaining such a valuable ATAC-seq analysis package!
I would like to know how to call peaks with only nucleosomal free reads and identify maker peaks.

I aim to compare motif enrichment results across species. However, I observed that distinct fragment length distribution across my snATAC dataset, which I believe was caused by the difference in the sample quality. The peak calling with nucleosomal free reads would avoid such technical confounds and make a reasonable comparison of TF motif enrichment.

[rcorces]

this functionality is not available in ArchR. You would have to filter your fragment files yourself if you only want to focus on sub-nucleosome reads.

[Y-ogativity]

I see. Thank you for the quick reply.