[Q] Question on normalization between 2 conditions before coolpups

[Lucas446]

Hi,

Thank you so much for providing this program it is very useful !

I performed HiC experiment and process the sequencing raw data using Juicer (.hic) and Hicexplorer (.h5 and .cool).

I have 2 replicates per conditions and I would like to perform pileup analysis on a set of 1000 small regions (.bed file) and comparing the level of interaction of this set between WT and Mutant.

I am not completely sure how the HiC data input should be normalized to perform WT.vs.Mutant comparison. I know that HiCexplorer has hicNormalize and hicCorrectMatrix tools, and other program such as in MultiHiCcompare perform a cyclic_loess normalization.

What do you do when you want to compare the result of coolpups between conditions ?

Thanks a lot for your help,
Best,
Tanguy