Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of Quercus acerifolia, and have aligned my paired-end NextRAD reads (filtered using process_radtags) to a reference genome (Q. robur) using GSNAP. The goal is to measure how many wild alleles are observed (captured) within garden samples. To this end, I want to generate a catalog of wild loci, a separate catalog of garden loci, and then measure the proportion of wild loci observed in the garden catalog.
My question is: how can I match RAD loci that were generated in separate catalogs? For instance, can I use adegenet to read in the files generated by Stacks and match the names of loci, since both garden and wild samples are aligned to the same reference (using the same parameters)?
My preference is to do this in R (ideally with adegenet, but open to other approaches). If not, is there a way I could just compare across 2 loci catalogs (i.e. find matches between two .fa.gz files)?
Thanks for any tips!