I have data from ddRADseq and I want to analyze them with stacks. I have reads of 33 individuals (2 parental and 31 backcross progeny ) the parents are of different species, therefore, my progeny is a mixture of two genomes (with a greater % of one kind of genome because they were several generations of backcross), I have the reference genomes of both parents. The idea is to search for a parent's loci (parental 1) in the genetic background of parental 2 I thought to start running the pipeline by hand using the command ustacks, (without the reference genomes since they are from different sp), and then make the catalog with cstacks using only the parental, finally with sstacks compare all the progeny with the parental catalog. Any recommendation? help!! Thank you!