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  • Mapping reads to find coding regions

    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

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