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  • diff_gene output from Cufflinks and Gfold to Entrez Gene ID

    Hi,
    I work on S. pombe. I mapped and analysed my RNA-seq using Tophat, cufflinks and cuffdiff. In a separate analysis I used GFOLD since I have only one replicate, to find differentially expressed genes. And I used Ensemble annotations.
    Now I want to analyze gene enrichment. I need a bit of detailed assistant on how to carry on from this step. I guess I need to convert Ensemble gene IDs to Entrez gene ID first? And then use that for gene enrichment analysis. If that is correct I don't know how exactly it is done. I tried DAVID Gene ID conversion, but when I load my file it says "You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type."
    So I have no idea what should I do to convert the IDs.

    Thanks,
    Parham

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