I am attempting to run Macs2 CallPeaks on some multiome data and running into a problem when attempting to run CallPeaks command on multiple fragment file paths in Seurat object.
peaks<-CallPeaks(DataCombined, macs2.path = "/anaconda3/bin/macs2")
FileNotFoundError: [Errno 2] No such file or directory: '/Users/Desktop/multiome/sc291/atac_fragments.tsv.gz /Users/Desktop/multiome/sc292/atac_fragments.tsv.gz /Users/Desktop/multiome/sc293/atac_fragments.tsv.gz'
So basically its listing all three paths together as a single path, not sure how to resolve this. TIA