Entering edit mode
6.5 years ago
R.Blues
▴
160
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!
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.
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