Hi all, I am trying to figure out how to align loci to in silico digested fragments. I would like to map ~50,000 loci from an RRBS experiment back to the fragments which resulted from the restriction enzyme digestion, but I am not sure how to do it. My goal is to determine if the loci are localized to a particular fragment size and/or a particular location within each fragment (ends, middle).
I have found many software packages that do in silico restriction enzyme digestions on the whole genome, but so far I am only able to extract information about the length of the fragments and start/end locations, not create files (fasta files of each fragment?) which I can align my loci back onto. Are you aware of any way this can be done?
Thank you in advance!