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  • Cufflinks to find introns, sequences look wrong?

    Hello,
    I'm using a TopHat, Cufflinks pipeline to find intronic sequences for a species I am interested in. I run TopHat, then run Cufflinks with -G option. I paresd out the exon boundaries then took the sequences between the exons and called those "intron" boundaries, but none of the sequences look as they should (mainly GT-AG for introns) and neither do the exons look to start or end with start/stop codons. I'm not sure if I've done something wrong or if I'm just running TopHat and Cufflinks wrong and parsing incorrectly. Any help is great!

    Best,

    anzdro

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