How to generate contact probability graph from mapped reads?

Question

[shaikh.zhas]

I have generated bam file from paired-end reads, now I want to see how much those reads are contacted, therefore I need tool for getting contact probability graph.

[Gabriel R.]

What do you mean by "contact"? overlapping?

Answer 1

[Anton Goloborodko]

Hi! Sounds like you are trying to assemble a map of 3d interactions from a sequenced Hi-C library? There is quite a few pieces of software that can help you out with this task: http://data.genomegitar.org/4DN_software.php. Our lab is developing a python library hiclib, which I could recommend, and there is many great alternatives, e.g. Homer, HiC-Pro, Juicer/Juicebox, hicpipe, etc.