Dear Steve: This is exactly why I can only get FASTA sequence but not hg19 sequence. I have sequence, but how can I print it out with hg19 coordinates next to it? Many thanks, Lan Ko
-----Original Message----- From: Steve Heitner [mailto:[email protected]] Sent: Tuesday, June 26, 2012 7:16 PM To: Ko, Lan; [email protected] Subject: RE: [Genome] hg19 Hello, Lan. If you have a list of genomic coordinates, you can use our Table Browser to obtain the sequences. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. To obtain the sequences, perform the following steps: 1. Go to http://genome.ucsc.edu/cgi-bin/hgTables 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: Click the "define regions" button to paste or upload your list of coordinates Output format: sequence Output file: Leave this blank to view the results on the screen, otherwise enter a filename to save your results to a file 3. Click the "get output" button 4. Select "genomic" and click the "submit" button 5. Select your desired options and click the "get sequence" button Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Ko, Lan Sent: Tuesday, June 26, 2012 3:15 PM To: [email protected] Subject: [Genome] hg19 Dear UCSC: I need to get a gene sequence with hg19 coordinates but not FASTA format. How should I download from your browser? Thank you. Lan Ko _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
