Hi all! First time poster.

I'm trying to come up with some metrics I could use for analysing and comparing Hi-C reads (which are being called as peaks in a manner similar to ATAC-seq peaks). As well as comparing the Hi-C peaks to ATAC-seq peaks. I've thought of a few already.

Metrics

• Overlap between TR pairs for an individual
• Overlap within one TR pair between individuals
• Combine all three TR pairs within each individual, then compare combined peaks between individuals.
• Overlap/total peaks within an individual
• Overlap/total peaks between individuals
• Genomecov TR pairs for each individual
• reldist for each TR pair within an idividual
• reldist for TRs combined within individuals (will this make the previous metric obsolete?)
• Reads per stage of pipeline
• picard QualityScoreDistribution (useful for assessing general quality of peaks?)

Thanks in advance!