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  • nmfly
    Junior Member
    • Jul 2012
    • 4
    #1

    Drosophila Reference gene annotation when using Cufflinks...

    Hi,

    I am very new and very much a beginner when it come to NGS technologies. I have aligned my RNAseq reads to the dm3 genome in galaxy (UCSC dm3 Drosophila annotation). For some reason the gene_ids are all annotated as CUFF.6 or CUFF.1 etc. but I would hope and expect gene-ids to be CG numbers from the annotation...

    Would anyone know what I have done wrong?

    Thanks in advance for any insight
    Last edited by nmfly; 07-19-2012, 03:34 PM.
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