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  • Annotate diff files

    Perhaps this is a better place to ask this question:

    I've run cuffdiff on my RNA-Seq data using UCSC_Genes.gtf as my transcript reference, and looked at the file gene_exp.diff. Here I see that the columns test_id and gene_id are both based on UCSC gene IDs, of course. How do I annotate this output in such a way that I can also see Entrez gene IDs there?

  • #2
    Unless you are looking for a programmatic solution see this.

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    • #3
      Thank you. I just understood after reading through that response and doing a bit of googling that I've been using the wrong term. Apparently it's not "Entrez Gene ID" I am looking for, but "Approved Gene Symbol". I.e. how do I annotate from the UCSC id "uc001fbz.3" to the gene symbol "S100A4" for example?

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      • #4
        Then this is what you need http://seqanswers.com/forums/showthread.php?t=22336.

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        • #5
          Yes! Great, that does look like what I'm looking for. Thanks

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