Hi! I've got two sets of replicate (x3) HiC libraries. I think I've set the min.inward, min.outward and max.frag thresholds for them correctly (or at least for the bulk of the datasets - not sure if I should set the threshold for replicate 3 individually?).
My question is: what is going on with these HiC libraries? Why do these peak heights look so different? Are any of the libraries "better" than the other ones? Are they usable?