Hi Lili, The funny chromosome names are explained on the Genome Browser Gateway page for each assembly. Here is a linked to the hg19 gateway page:
http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19 Scroll down and you will see a section called "Chromosome naming scheme". Hope that this information helps to clarify things for you. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Lili Li <[email protected]> Date: Tue, Nov 22, 2011 at 12:36 PM Subject: Re: [Genome] Gene track file To: "[email protected]" <[email protected]> Thanks for the information! One more question: After I downloaded the table with selecting a couple fields, e.g. Refseq and geneSymbol, I noticed that there are a lot of blanks in Refseq column and on Chromosome column, there are chr6 and chr6_apd_hap1 with the same refseq ID, but totally different start positions . What I want are the unique Gene ID, Chrom, strand, start position of genes and end position of genes. Could you please explain those table for me. Should I consider chr6 and chr6_apd_hap1 the same since they have the same refseq IDs. Lili From: Greg Roe [mailto:[email protected]] Sent: Monday, November 21, 2011 7:11 PM To: Lili Li Cc: [email protected] Subject: Re: [Genome] Gene track file Hi Lili, You're on the right track. If the table you're interested in doesn't show gene names, for the output format in the Table Browser choose "selected fields from primary and related tables". Then you'll need to select a table that will have the gene name. For example, if you're using UCSC Genes (or RefSeq Genes), select the geneSymbol field from the kgXref table (along with the fields from the primary table you want) and get output. Please let us know if you have any additional questions: [email protected] <mailto:[email protected]> - Greg Roe UCSC Genome Bioinformatics Group On 11/21/11 11:37 AM, Lili Li wrote: Hi, I am interested in getting gene annotation file from Genome Browser, but when I went to Table browser and get output from there(track in text format), the output file didn't give me unique gene IDs. Would you please let me know where I can get this information from Genome Browser? Thanks for the help, Lili Li, PhD JMP Life Science Developer SAS Institute Inc, 100 SAS Campus Dr. Room T3134, Cary, NC 27513 Email: [email protected]<mailto:[email protected]> Phone: (919) 531-2662 http://www.jmp.com/software/genomics/ _______________________________________________ Genome maillist - [email protected]<mailto:[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
