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  • Uploading XLOC gene IDs to IPA

    I have excel files with gene IDs as XLOC... I found out they are genes detected through Cufflinks program for RNAseq data. I could not manage to upload them to IPA with this identifier. I also have the gene names in the excel file; however in that case it omits mapping of about 20% of the genes. Please help.
    Thank you

  • #2
    "IPA"? I presume you are talking about the software from Ingenuity Systems. If so, since this is commercial software with (we hope) good support then I suggest writing directly to them. You'll probably get better and faster answers.

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    • #3
      Originally posted by westerman View Post
      "IPA"? I presume you are talking about the software from Ingenuity Systems. If so, since this is commercial software with (we hope) good support then I suggest writing directly to them. You'll probably get better and faster answers.
      Last time I used IPA it didn't recognise XLOC ID's which I'm pretty sure are an internal tracking ID for Cufflinks and hence aren't directly transferable to gene names.

      I think the OP might want to cuffcompare to a reference GTF to provide meaningful identifiers for IPA. Or upload the 80% of his annotated data as gene names. IPA never manages to do 100% ID conversion to its internal identifiers anyway so there's always some attrition of data on import.

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