Hi-C, inferring contacts from normalized matrixes

Question

[R.Blues]

Hello everyone,

I am sorry for bothering you, but I would like to know if there is a simple way to infer, from Hi-C data, which bins are in contact with others, just using directly the normalized matrixes. In my case I am trying to do this with the 40kb bin size datasets of Ren Lab (http://chromosome.sdsc.edu/mouse/hi-c/download.html). I am not sure if there is a standard cut-off, or if there is another method that is typically used; I am afraid I am a bit lost.

I hope you can help me. Thank you very much for your time and help!

[Kay]

Hi Blues, I came across the same question right now as you, and I'd like to know whether you found the way already? Many thanks.

[R.Blues]

Hi Kay! I'm afraid it's been too long. Perhaps you could do a density plot of the values, and see what would be a good cut-off. Otherwise maybe check other papers and see what they do, or contact someone who knows more than me =P