lldelisle
commented
10 months ago Indeed, by default all tools in HiCExplorer will use weights if available. If you don't want to use them, please use hicConvertFormat with the option --load_raw_values to get a cool file without weights.
When hicNormalize normalizes cool, it seems use weight in cool for balance first, which results in most of the bin values becoming 0 when using the '-sz 1.0 --normalize smallest' parameter.I think that normalizing cool should be done without balance, or provide an optional parameter.