My HiC library was prepared using two restriction enzymes. The HiCExplorere tool findRestSites seems to take only one enzyme site as input. Is there any way I can use two restriction enzymes and analyze my data using HiCExplorer.
I was able to generate the list of restriction fragments (bed file) after genome digestion using two restriction enzymes used in Arima HiC kit. I used HiC-Pro digest_genome.py to do that (https://github.com/nservant/HiC-Pro). Arima kit uses two restriction enzymes ^GATC and G^ANTC. Since digest_genome.py does not allow for "N" in the cut sites. I used following command to get around this problem: