I was trying to make sense of the RiP% value that is returned by ChIPQC. I understand that this is basically just a percentage of how many reads are located within the called peaks.
The vignettes indicate that a RiP% of 5% or greater is typically indicative of good enrichment. For some of the samples I processed I am seeing values as great as 22%. for the 30 samples I am analyzing, the RiP% values range from 13.4 to 22.9. My first instinct was, "Great! Higher RiP% value = greater enrichment!". However, as I think about this a little more I have become slightly concerned that the high RiP% values I am observing could be the result of insufficient stringency in peak calling. Having less stringent peak calling parameters might lead to a greater number of reads occurring in peaks simply because a greater number of peaks are being called. Is this a reasonable train of thought? Are these high values something to be concerned about? My thought is that this would definitely have a substantial impact on the identification of differential peaks down the line.
Any information on how to best go about thinking about this or if this is even a problem is appreciated!