Hi community!
It has been a while since I've updated myself on Hi-C (bulk) analysis methods. I was wondering if you could please help me find out which methods/tools exist to calculate statistical significance for each interaction in a Hi-C matrix, the point is that we can filter out nonsignificant interactions or interactions that might be random. What are people doing nowadays?
Do people do this on a per-network (case-by-case) basis? or is it by comparing one phenotype to another phenotype? I guess both things are possible, but I don't know which tools people use now.
Do the methods consider the linear distance for intrachromosomal interactions? Are the Hi-C matrix counts typically modeled using a particular distribution or are inferences made for each dataset because sequencing depth could affect it so much?
I guess I am just asking your help please with knowing what is out there, I'll be grateful for your help!
Thanks!!
