Hi Shamsher, In the table browser, for the output format setting, select "selected fields for primary and related tables", as I think you were doing already. On the subsequent screen, select the fields you want from the primary table at top, but also see the next table down, called hg19.kgXref fields. In that table, select the field called Gene Symbol. I believe that's what you are looking for. Though you can select other IDs there too (e.g., RefSeq) as well as some annotation information (i.e., Description). Then "get output" as usual.
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 6/6/11 8:08 AM, shamsher jagat wrote: > I am not sure Swing was having string of my messages. But I can explain one > more time, I want to donwload list of all TSS for human genome which Swing > explained to me how I can get list of all TSS. When I downlaod the list of > such TSS I have coordinated (Chro no and start and end position) but no > gene. enetrz gene ids to which such TSS is attached. My question is how can > I have list of corresponding gene ids with list of TSS. > Hope this will help. > Thanks > ---------- Forwarded message ---------- > From: Katrina Learned<[email protected]> > Date: Fri, Jun 3, 2011 at 2:15 PM > Subject: Re: [Genome] Downloading TSS for list of genes > To: shamsher jagat<[email protected]> > Cc: [email protected] > > > Hi Shamsher, > > I'm sorry, but I am having trouble understanding your question. Do you want > to obtain a list of only the TSS you are interested in with information > about the gene? Or, do you want to get a list of all the TSS with > information about the genes? > > Also, can you be more specific about what information about the gene you are > want your results to include? > > Please reply to the mail list ([email protected]). > > Thank you, > > Katrina Learned > UCSC Genome Bioinformatics Group > > shamsher jagat wrote, On 06/03/11 06:25: > > Thanks for your quick and detailed answer. this is the first time I have >> recieved reply that quickly from your list >> How will I get corresponding gene annotation. Is there any way that I can >> get annottaion corresponding to TSS site ? Instead of looking at my >> selected >> list I am downloading all the Tss and than quary with my list. So if I can >> map the gene names that will be greta. >> >> Thanks >> >> On Thu, Jun 2, 2011 at 12:20 PM, Vanessa Kirkup Swing >> <[email protected]>wrote: >> >> >> >>> Hi Shamsher, >>> >>> The best way to go would be to use the table browser. To get to the table >>> browser click on the "Tables" from the blue navigation bar. To get the TSS >>> based on UCSC Genes set the following: >>> >>> clade: Mammal >>> genome: Human >>> assembly: hg19 >>> group: Genes and Gene Prediction >>> track: UCSC Genes >>> table: knownGene >>> region: genome >>> identifiers (names/accessions): (paste or upload list) >>> output format: selected fields from primary and related tables >>> >>> Click "get output" >>> >>> Check the fields that you want to be displayed (here are some that I would >>> select) >>> name Name of gene >>> chrom Reference sequence chromosome or scaffold >>> strand + or - for strand >>> txStart Transcription start position >>> >>> Click "get output" >>> >>> This should display all the genes that you pasted in along with their >>> transcription start sites. >>> >>> Also, you might want to take a look at the following TSS tracks under the >>> "Expression and Regulation" subsection of the >>> browser track controls: >>> >>> 1. SwitchGear TSS (hg18& hg19 assemblies) >>> 2. Eponine TSS (hg19 assembly) >>> >>> Hope this helps you! If you have further questions, please contact the >>> mailing list: [email protected]. >>> >>> Vanessa Kirkup Swing >>> UCSC Genome Bioinformatics Group >>> >>> >>> ----- Original Message ----- >>> From: "shamsher jagat"<[email protected]> >>> To: [email protected] >>> Sent: Thursday, June 2, 2011 10:39:04 AM >>> Subject: [Genome] Downloading TSS for list of genes >>> >>> I want to have list of TSS for number of human genes (1000) what should be >>> teh best way to go. >>> >>> Thanks. >>> _______________________________________________ >>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
