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  • Finding Exon-Intron Junctions without a reference genome

    Hi,
    I'm trying to find intron-exon junctions in assembled transcriptome data without a reference genome. Does anyone know of a tool that can do this?

  • #2
    In general this is an underdetermined problem; most of the information for making the splice lies in the introns. There is a weak signal left behind, but not much.

    Your best bet is probably to compare your assembled RNA to the closest relative you can find with this information.

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    • #3
      Finding Exon-Intron Junctions without a reference genome

      Thanks for the advice. I'll try using a relative.

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      • #4
        Hi,

        You may try Cufflinks or Scripture to let the software figure out the intron/exon junctions for you.

        Douglas

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