Hi Jun, An explanation of the coordinate system we use in the tables/annotation files vs. the display is here:
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 and more information is here: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/27/12 10:12 AM, Jun Lu wrote: > Hi, > I am looking at the downloaded tRNAs.txt file for hg19, and there is 1 > base difference associated with End position on chromosome (but not > Start position) for tRNA entries. > > One example is chr1.tRNA136-AsnGTT, for which the tRNAs.txt file > (downloaded yesterday, with a time stamp of 2012-2-13) showed the > following record: > > 713 chr1 16847079 16847153 chr1.tRNA136-AsnGTT > 1000 - Asn GTT No canonical tRNA introns</BLOCKQUOTE> > 77.65 http://gtrnadb.ucsc.edu/Hsapi19/ > http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.ht > ml#Homo_sapiens_chr1.trna136-AsnGTT > > So considering the 0-based position information in annotation files, I > was expecting that this gene will map to chr1:16847080-16847154. > However, on genome browser, this gene (chr1.tRNA136-AsnGTT) is shown as > chr1:16847080-16847153 > <http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=262084701&db=hg19&position=chr1%3A16847080-16847153>, > which is different for 1 base at the End position. > > I did notice that the tRNA track on genome browser display shows > 2012-02-02 as the updated date. Is this the reason for this discrepancy, > or there is something I misunderstood from the tRNAs.txt file? > > Thank you, > > Jun > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
