From: shamsher jagat <[email protected]> Date: Thu, Jun 2, 2011 at 4:04 PM Subject: Re: [Genome] Downloading TSS for list of genes To: Vanessa Kirkup Swing <[email protected]>
Thanks for your quick and detailed answer. this is 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
