On 3/9/11 1:29 PM, Vanessa Kirkup Swing wrote: > Hi Duke, > > Here is an easier way to get the 3' UTR sequences with refSeq ID's. > > In the table browser, please select the following: > > group: Genes and Gene Prediction track > track: RefSeq Genes > table: refGene > region: genome > output format: sequence > > Click "get output" > > Select: "genomic" > Click "submit" > > Select: "3'UTRs" > Click "get sequence"
Thanks so much Vanessa. It works perfectly! D. > Hope this helps! Please contact the mailing list if you have further > questions. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Duke"<[email protected]> > To: [email protected] > Sent: Tuesday, March 8, 2011 2:33:26 PM > Subject: [Genome] Extract 3' UTR sequence with refSeq > > Hi, > > Following this > (https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008882.html) > instruction, I was able to extract the 3' UTR sequence from Table > Browser, but the fasta headers are gene ID and other infos (for example: > ">mm9_refFlat_Xkr4 range=chr1:3204563-3206102 5'pad=0 3'pad=0 strand=- > repeatMasking=none"). > > Please let me know a proper way of getting 3' UTR but with refSeq IDs > instead of gene IDs. Converting from gene ID to refSeq in this case > seems not to be a solution since there are lots of identical gene IDs > (and range etc...). One example would be: ">mm9_refFlat_Tcea1 > range=chr1:4886446-4887990 5'pad=0 3'pad=0 strand=+ repeatMasking=none" > (there are three such identifications). > > Thank you in advance, > > D. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
