Analysis pipeline for 3e Hi-C

Question

[ancient_learner]

Hi

I recently came across with this paper in which Chromatin was subsequently digested with three enzymes. According to my knowledge the restriction site is pretty much used in QC to obtain valid Hi-C pairs. But since, they have used 3 enzymes I am unable to find how they filtered the sequenced data based on restriction digestion and how Hi-C fragments are identified. Any clues or ideas would be appreciated.

[Gautier Richard]

I guess that since they know the restriction site of these 3 enzymes, instead of keeping reads with the pairs having the usual DpnII or HindIII restriction site, they looked for pairs showing either one of the 3 restriction sites?

[ancient_learner]

Could be. But What would be the advantage of such approach?

[Gautier Richard]

The idea might be to increase the resolution of Restriction Fragment length binned Hi-C matrices.

More restriction sites = smaller bins = higher resolution. I don't know if it helps them to identify new features though.