Annotate diff files

[cnyh]

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]

Unless you are looking for a programmatic solution see this.

[cnyh]

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?

http://www.genenames.org/data/hgnc_data.php?hgnc_id=10494

[GenoMax]

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

[cnyh]

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