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  • How to convert mapped ESTs to genome information into transcripts?

    Hello, I am very confused, I have RNA-seq data and I have mapped it to my assembled genome (still a few hundred contigs) so I have got about 20000 mapped contigs. My question is how can I translate that into transcripts? I mean how can I know two or more contigs belong to the same transcript. Is it possible to know how many genes do I have? Can I use that information to annotate my genome? I have annotated it with predictions and I was expecting to keep only the predictions that I have evidence for in my RNA-seq data but I don't know how to do that. How to make that link? Any help will be very much appreciated, thanks.

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