Hi,

I've been working with bulk and single-cell ATAC-seq data for some time now and was wondering about the theoretical reasoning behind ATAC peak signal strength in single cells. In theory, if you look at a single cell you should have a binary signal for each genomic region - chromatin is open ("1"/"yes") or it is closed ("0"/"no"). While I think I understand how you practically still end up with lower and higher peaks in each cell due to library amplification, cluster generation etc., I was wondering whether it is more appropriate to handle peaks' counts as continuous or to convert them to binary signal when comparing cells/samples and how different single-cell analysis software handles this.

Thanks a lot!