Hi-C hicexplorer how to compare 2 hi-c matrices?

Hi :slight_smile:
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.

Best,
D.

Hi Dotkom,

Call TADs in one sample and run the differential TAD analysis with hicDifferentialTAD. With this you can check if the called TADs in one sample, or to be more precise, the Hi-C interaction strucure, differes between the samples. You can run hicPlotSVL to compare the global short vs. long distance interaction ratio, you can use hicAverageRegions and hicPlotAverageRegions to see if there is a global change in the TAD pattern between samples. You can compute the A/B compartments and plot the matrices, the TADs and the compartments, and plot all this data with pyGenomeTracks.

Best,

Joachim