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cnyh 03-08-2013 07:49 AM

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?

GenoMax 03-08-2013 07:55 AM

Unless you are looking for a programmatic solution see this.

cnyh 03-08-2013 08:18 AM

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?

GenoMax 03-08-2013 09:55 AM

Then this is what you need

cnyh 03-08-2013 09:59 AM

Yes! Great, that does look like what I'm looking for. Thanks :)

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