I have gone through diffHiC to get significantly interacting bins in my data set. Next, we want to be able to confirm some of these interactions with PCR. To do this properly, I need to be able to see what specific fragments or reads in our significant bins that are doing the actual interacting. Preferably, I'd like to get the pairs of actual RE sites that are ligated together, but the ligated fragments will do. Is there an easy way to extract this information from one of the data objects? I was going to check out connectCounts and feed it the fragments in the significant bins as regions, but would appreciate any input if anyone has done something similar.