We are working with capture Hi-C data sets where we have designed baits to all human promoters. In most cases, each promoter has at least two MboI fragments that contain a bait due to our design strategy. This results in interactions with distinct ends over promoter regions, leading to some redundancy in our interactions, thus we would like to limit each promoter region to just one "fragment."
As a test, we merged MboI fragments that contain a bait over the promoter and generated a new rmap file that essentially has one long fragment over each promoter. Obviously this results in a larger number of reads mapping to each promoter fragment since now a fragment represents two or three MboI fragments.
Chicago finds ~2/3 of the same interactions with both rmap files (original MboI and altered promoter MboI), but there is a substantial number of interactions that are different between them. Can you provide any suggestions or insights as to how this manipulation may affect how Chicago calls interactions and whether this approach is correct or contains problems?
Thank you very much.