I am new in working with Hi-C data and I was wondering how I could do a QC on it. I do not mean to know the sequencing parameters and so on, but to know if all my genome is well represented within this data. I aim to use Hi-C data for scaffolding a de novo genome and I need to know if the data is good. I've just found this software (
https://github.com/cerebis/qc3C) but in the absence of a reference genome (as it is my case) you need to input the enzymes you used for digestion, and in my case the protocol is enzyme-free. Any suggestions? I would be extremely grateful!!
Thanks in advance!