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 ?
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