HiCExplorer final mcool file load in GENOVA

[usernicai]

I recently worked on cool files between GENOVA and HiCExplorer. I first converted the matrix file from hic-pro to cool file. Then we use HiCExplorer's hicNormalize and hicCorrectMatrix (--correctionMethod KR). Can the resulting cool file be directly used for downstream analysis in GENOVA? Do I still need to select balance=T at the beginning of load_contacts?

[teunbrand]

I guess this should work if you set balance = TRUE and there is a KR slot in the hdf5 file.