Hello, I have two interaction files for two different stages S1 and S2 as obtained from HiCHip data and have analysed it. I have associated Gene annotations to the chromosome regions wherever possible. I want to plot contrasting interaction profiles which are lost/gained in the two stages, but not sure where two start from
My interactions are in this form
Chr1 Start End Chr2 Start End Gene1 Gene2 Some_Score(q value/z-score)
As an example, I have attached an image from the paper Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Rubin et al., Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14. Any leads will be very helpful.