We downloaded fragment files for four human PBMC scATAC-seq datasets from the 10x Genomics website and combined the four files into a single fragment file, adding a prefix to the cell barcodes to mark which cell originated from which dataset. We called peaks using the combined dataset with MACS2, using the CallPeaks function in Signac. Peaks overlapping genomic blacklist regions for hg19 were then removed61, resulting in a set of 160,906 peak regions.
