Hello,

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.

Thank you,

~ Heather

The easy way is to use extractPatch with width=1, which should effectively pull out counts for interactions between pairs of specific restriction fragments.

The harder way, if you want the original read positions, is to use loadData for a specific chromosome pair, and then identify the rows with anchor indices that point to the desired restriction fragments in param$fragments. From there, you should be able to figure out which ends are ligating to each other.

I must admit that I've never done this procedure, which is why it requires some manual work. I may add it if it seems useful, but most interactions span several kilobases at least (and usually several fragments as well) so base pair resolution was unnecessary in most cases. But I guess if you're spending good money ($100?) to design some primers, you might as well do it on the ligation products that you're most likely to observe...