ICE Normalization for HiC Dataset Comparison

[hanbinlu]

I am thinking how should I do if I want to compare 2 experiments with different sequence depths. Here is two ways come up to me but I am not sure whether they are correct:

1. Set the total_counts parameter of each experiments's normalization be the same. Then I can compare the normalized counts of them?

2. Output the bias of each experiment. And transform the raw count map into probability matrix by calculating Tij=Oij/BiBj. Is this calculation for probability matrix correct? Or there is some ways to calculate the probability matrix from the output normalized count matrix?

Thanks

[NelleV]

Hi @sf-nevermore
I am terribly sorry: I am only just seeing this ticket.
For comparing two contact maps, I'd suggest using a differential analysis tool. A couple have been published for Hi-C data and they should deal with sequencing depths differences.

Thanks,
Nelle