Can I use hic-pro for Hi-C 3.0 ?

[hanshanmengqi]

Hi,

Thanks for developing such a helpful tool! But I saw a paper (https://www.frontiersin.org/articles/10.3389/fpls.2023.1223591/full) that said hic-pro is unsuitable for Hi-C 3.0. Because Hi-C 3.0 involves fragmenting with two enzymes and hence a diversity of ligation events.

So, what do you think?

Best, Han

[nservant]

Hi, The digest_genome.py file can support multiple restriction enzymes, so as soon as you do have the restriction fragment digested with all these enzmes, I do not see why HiC-Pro could not work ... For instance, HiC-Pro was successully used with the Arima kit which is based on multiple restrictions ... Best Nicolas