Dear Rahil, One way is to look at the track description page in the genome browser for the track you are interested in. Here is an example using the human hg19 UCSC Genes track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=knownGene Click on "View table schema" which will get you to this page: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema If you scroll down you will see this statement: Note: all start coordinates in our database are 0-based, not 1-based. See explanation here. Here is a link to the explanation: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 Hope this helps. Please contact the mailing list again if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: [email protected] To: [email protected] Cc: [email protected], [email protected] Sent: Thursday, September 30, 2010 6:03:41 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Postions of genome and annotated genomic regions zero based or one based in UCSC Genome Browser? Hello, I would like to know whether the positions of genome and annotated genomic regions such as exon start and stop positions, CDS start and stop positions, transcript start and stop positions, extracted from either Tables or ftp of UCSC Genome Browser, are 0 based (considering start position of the genome as zero) or 1 based (considering start position of the genome as 1)? I would like to know especially for human genome. Such information about other genomes will also be helpful. Thank you, Rahil Sethi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
