Uploading XLOC gene IDs to IPA

[fozturk]

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

[westerman]

"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.

[Bukowski]

"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.