Hi Danielle, The kgXref table contains a geneSymbol field (that has the HUGO gene symbol when available) and the RefSeq accession number. You can download a dump of the table, kgXref.txt.gz, here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/3/11 7:42 AM, [email protected] wrote: > Hi Vanessa, > > Thanks so much for your quick response (and sorry for my slow one!). > > The URL is http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ > > This contains the upstream1000.fa.gz file. The names are in RefSeq accession > numbers, and the only keys I can find must be from different versions because > not all genes are covered (I am looking for the HUGO symbol). I was hoping > you guys might have a file that could easily be merged with the RefSeq > accession numbers as opposed to compiling my own from various versions of > RefSeq Id's. > > Thank you. > > Danielle > > Quoting Vanessa Kirkup Swing<[email protected]>: > >> Hi Danielle, >> >> Can you please provide us with more information so that we can >> understand your issue such as the link to the file >> (upstream1000.fa.gz), which genome and assembly this file is from and >> which RefSeq IDs you are referring to? Please respond to the mailing >> list: [email protected]. Thanks! >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ---------- Forwarded message ---------- >> From:<[email protected]> >> Date: Thu, Sep 29, 2011 at 12:15 PM >> Subject: [Genome] Fasta Sequence >> To: [email protected] >> >> >> Good Afternoon. >> >> When working with the file "upstream1000.fa.gz" I have been able to >> use it for analysis and it is in a great format, however, I was >> wondering if you had the conversion for RefSeq ID to Gene Symbol Id. >> The reason I ask is all of the databases I can find have updated >> RefSeq ID's (of which only 5000 match), so I am unable to translate >> easily. I have a program for analysis, so if you have the upstream >> file with updated RefSeq ID's that would also be great. >> >> Thank you. >> >> Danielle Barnes >> [email protected] >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
