Calculate QC metrics (Nucleosome signal, TSS enrichment, FRiP, etc) before or after merging multiple datasets?

[rgdani]

Hi! Thank you so much for developing Signac. Not only has the tool been incredible for my research, but I really appreciate willingness of the developers to answer our questions!

I am currently working on integrating the ATAC part of my 10X multiomics datasets. I have 2 datasets to integrate, I want to remove the low quality cells prior to integrating. However, I am not sure as to which approach I should take.

I am planning to filter the cells based on FRiP, blacklist ratio, TSS enrichment, nucleosomal signal. Should I calculate these features on each seurat object, merge, and subset OR should I merge, calculate the features and subset?

[timoast]

Either is fine, usually I do QC on each object before merging.