I have mapped RAD-PE reads to a reference genome (that consists only of scaffolds without the assignment of scaffolds to any chromosome) and called SNPs. However, in order to answer my research question I now need to align reads (that are now mapped to reference genome scaffolds) to the Zebra Finch genome (as this is the closest complete genome to my study species).
My question is that what the best software (and method) to do this?
Thank you very much for your help in advance
p.s. I am relatively new to bioinformatics!