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robinweide / GENOVA

GENome Organisation Visual Analytics
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HiCExplorer final mcool file load in GENOVA #346

Open usernicai opened 6 months ago

usernicai commented 6 months ago

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 commented 6 months ago

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