can someone help me with the analysis of Hi-C data? I am trying to compare chromatin structure and characteristics between my treated and untreated sample. I have corrected matrices and I can perform hicCompareMatrices … and then what? Can I call TADs from the result of matrix comparison? Or should I call TADs in one and the second sample and then… and then what? Compare coordinates of TADs?
Could you please help me? In the end I would like to see if changes in histone marks are limited or not to TADs that changed after treatment.
I would be very grateful for any help.