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7.0 years ago
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Hi,
I was asked to check coverage inside peaks I've called using macs2, when I calculated the average read depth in each peak, the IP average was lower than input average in the same interval (for example, if my IP had an average of 18, the input was 44). I used coverageBed to check read depth. Does macs2 normalize the data in a way that might explain this? It is not due to library size, while input was 3 times larger, it still doesn't seem to account for the differences... thank you for your help!
if anyone is interested, the macs algorithm is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592715/