Mapping reads to find coding regions

[Diede]

Hi all,

I recently did a ddRAD study of a specific mussel species (which doesn't have a reference genome yet), and now I want to see if I hit any interesting coding regions with my RAD markers. I used BLAT to map my reads to four different bivalve mollusc genomes and have obtained the coordinates of quite some hits. I know would like to see whether those coordinates of the genomes are located in gene regions.

Does anyone know how I can tackle this problem?

Best, Diede