Hello, I am performing 5C analysis using the forward and reverse primer interaction matrix(reads sequenced per primer combination). I have isolated all the interactions of the specific forward and reverse primers which overlap with a set of enhancer coordinates using my5C.webtools making a new subset matrix. I would like to know if there is an efficient way to group(add the interactions of forward primers and add interactions of reverse primers) the interactions corresponding to an enhancer giving me a matrix of enhancer interacting with enhancers alone and not in terms of the primers. This would have to be done manually by finding out the overlapping primers with the enhancer bed file and then adding the rows and columns of the corresponding overlaps for each enhancer. But I have a set of 50 enhancers. Is there a tool that I could make use of or an R script for the automation? Input data that I have: Interaction matrix, enhancer coordinate bed file with names.
Thank You in Advance