Annotate diff files

cnyh · 03-08-2013, 08:49 AM

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, 08:55 AM

Unless you are looking for a programmatic solution see this.

cnyh · 03-08-2013, 09:18 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?

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

GenoMax · 03-08-2013, 10:55 AM

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

cnyh · 03-08-2013, 10:59 AM

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

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03-08-2013, 08:49 AM	#1
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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?

03-08-2013, 08:55 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Unless you are looking for a programmatic solution see this.

03-08-2013, 09:18 AM	#3
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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_d...?hgnc_id=10494

03-08-2013, 10:55 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Then this is what you need http://seqanswers.com/forums/showthread.php?t=22336.

03-08-2013, 10:59 AM	#5
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	Yes! Great, that does look like what I'm looking for. Thanks