Currently I am in the process of analyzing HiC data from two different conditions. When I talked to some colleagues about best way of analyzing and comparing two HiC data-sets, I was asked to look at the `diffHiC`. I read the user-manual and the paper. Congratulations on the paper. I have a question. The paper starts with reads or `bam` files. What if I already have to HiC interaction matrices from two different conditions. Can I still use `diffHiC`? I did not see a simple path to do that. If I am missing something please point me in the right direction. Any help in this regard is highly appreciated.
What I have used is `HiCPro` (the first author of this paper also suggested that I use `diffHiC`) to process the data. Each data has ~5 B reads. I have already aligned and generated ICE normalized contact matrices. There is quite a bit of difference between the two interms of read-depth. When I plotted them using `HiCPlotter`, I can see that there are differences, but I would rather have some kind of statistical measure/FDR for those differences so that I can explain to the collaborator how to interpret that data.