Should I compare Hi-C matrices before or after normalization?

Question

[manuel.fernandez]

Hello,

I want to compare two Hi-C replicates to see if they are similar enough for pooling. I plan to do so using the suite of reproducibility analysis 3DChromatin_ReplicateQC (https://github.com/kundajelab/3DChromatin_ReplicateQC). Should I compare the matrices before or after normalization? (I'm using ICE)

Thanks, Manuel F. Merino