Hi Pauline, Thank you for the very helpful information. Based on your info, I have checked some mrna, est and cytoband position on the Genome Browser and compared the results with the data in data files. They are all 0-based start and 1-based stop as you specified.
Thank again for the help. Liqun -----Original Message----- From: Pauline Fujita [mailto:[email protected]] Sent: Wednesday, September 22, 2010 3:08 PM To: Qi, Liqun (NIH/NCI) [C] Cc: [email protected] Subject: Re: [Genome] a question about one or zero based coordinates Hello Liqun Qi, These files are just dumps of the database so they are also zero-based start and you will have to add 1 to see 1-based starts. You can also double check the results by viewing them again in the browser. For more information on coordinates you can also see this wiki page: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 9/22/10 7:31 AM, Qi, Liqun (NIH/NCI) [C] wrote: > Hi, > > I am a database developer for NCICB(The NCI Center for Bioinformatics). We > use your three dump files (all_est.txt.gz, all_mrna.txt.gz and > cytoBand.txt.gz) of both hg19 and mm9 for our caBIO > project(http://cabioapi.nci.nih.gov/cabio43/Home.action). As you explained at > your FAQ site (http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1), "Our > internal database representations of coordinates always have a zero-based > start and a one-based end", should I add 1 for each start position for all > those three files in order to see the one-based start coordinates? > > > Thanks, > Liqun Qi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
