Hello! Any tool for the downstream analysis of the HiC Sequencing data requires the restriction enzyme which was used for generating the HiC data. Is there any way to get it from the Sequencing data? Can I get any information from the fastq files?
DpnII is/was used in my case, I had 'GATCGATC' ligation sites in my reads.
A good way to check this is to map your reads against a reference genome, and check if your mapped reads are split on GATC-GATC (or other enzyme site). The overhangs of the enzyme cut sites are filled in and ligated, so you can determine the enzyme site this way.
Or you can ask the supplier of the data off course ;-)