converting UCSC gene names to Hugo Symbol names

efoss · 07-16-2011, 01:31 PM

I am having a lot of trouble with getting the UCSC gene names converted to more normal names - like Hugo Symbol names. I have the kgAlias.txt file, but that file seems to match up UCSC names to quite a few other names, many of which are no more biologically meaningful than the original UCSC name. Can I download a file that is just like the knownGene.txt file (having gene name, chromosome, strand, transcription start, transcription stop, coding sequence start, coding sequence stop, number of exons, exon starts, exon stops, etc.) except where the gene name is a Hugo Symbol gene name?

Thank you.

Eric

kwatts59 · 07-16-2011, 01:35 PM

Try this site
http://genecards.weizmann.ac.il/genetide-bin/tide.cgi

efoss · 07-16-2011, 01:41 PM

Thanks. I'll look into that site.

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07-16-2011, 01:31 PM	#1
efoss Member Location: Seattle Join Date: Jul 2011 Posts: 98	converting UCSC gene names to Hugo Symbol names I am having a lot of trouble with getting the UCSC gene names converted to more normal names - like Hugo Symbol names. I have the kgAlias.txt file, but that file seems to match up UCSC names to quite a few other names, many of which are no more biologically meaningful than the original UCSC name. Can I download a file that is just like the knownGene.txt file (having gene name, chromosome, strand, transcription start, transcription stop, coding sequence start, coding sequence stop, number of exons, exon starts, exon stops, etc.) except where the gene name is a Hugo Symbol gene name? Thank you. Eric

07-16-2011, 01:35 PM	#2
kwatts59 Member Location: nevada Join Date: Apr 2011 Posts: 46	Try this site http://genecards.weizmann.ac.il/genetide-bin/tide.cgi

07-16-2011, 01:41 PM	#3
efoss Member Location: Seattle Join Date: Jul 2011 Posts: 98	Thanks. I'll look into that site.