First of all, thanks so much for making this great tool, keeping this up to date, and answering users' every single question!!
Can you clarify how Signal.UniqueMultiple.*.bg and vs Signal.Unique.*.bg files are made and what are the differences between these two files?
I assume that Signal.UniqueMultiple is from all aligned reads whereas Signal.Unique is only from uniquely-mapped reads?
Are these files simple base counts of Aligned.sortedByCoord.out.bam, with or without -q 255?