Hi,

During scATAC-seq data preprocessing, does it make sense to filter data matrix, so it contains only most variable peaks (in the same way how we do it for scRNA-seq), before any further dimensionality reduction or clustering analysis?

Thanks

You're not asking about a specific Bioconductor package; a general question should be posted on a more general forum like Biostars. But for what it's worth, the answer is: probably yes.