Peak calling can be performed in theory for any CUT&RUN or CUT&Tag dataset so long as two points are met:
First, the Unique BAM file to be used for peak calling originates from a quality sequencing event (details found on the Alignment Summary Report) e.g. acceptable read depth, % unique reads, SNAP-CUTANA Spike in recovery, etc.
Second, it is strongly recommended to use an IgG control reaction as the peak calling control to determine the background signal of the system. Selecting the correct IgG negative control is also important. For example, the wild type IgG should be utilized with target reactions in those cells, but a drug treated IgG should be used as the control for target reactions in treated cells.