According to the Chromvar vignette (https://bioconductor.org/packages/release/bioc/vignettes/chromVAR/inst/doc/Introduction.html), "If analyzing single cell data, it can make sense to use peaks derived from bulk ATAC-seq". The wording is confusing. Do they mean use annotation of peaks defined by bulk ATAC-seq as the 'reference' against which to align single cell ATAC-seq reads? Why can't we use a consensus peak set derived from the single cell data instead?
I've read the methods section of the Nature Methods paper (https://www.nature.com/articles/nmeth.4401#Sec3) and I'm still a little unclear on this.
Thanks for your help!