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  • brachysclereid
    Member
    • Feb 2011
    • 32
    #1

    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?
    Tags: None
  • krobison
    Senior Member
    • Nov 2007
    • 734
    #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.

    Comment

    • brachysclereid
      Member
      • Feb 2011
      • 32
      #3
      Finding Exon-Intron Junctions without a reference genome

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

      Comment

      • DZhang
        Senior Member
        • Jun 2010
        • 177
        #4
        Hi,

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

        Douglas
        https://www.contigexpress.com

        Comment

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