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Mapping reads to find coding regions

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SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)
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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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