Can my % edited cells and % edited alleles be directly compared across my samples?

The denominator of the percentages (total # cells or total # alleles) will likely be different across your samples because different numbers of cells may be assessed at each target site for each sample due to variability in sequencing depth. Therefore, check to see that at least 1,000 cells have been called by the cellfinder module (# cells metric on the “Summary Tab”). If one or more of your samples has <1,000 cells called, then use caution when comparing the % cells and % alleles with edits to other samples.