Hi Christopher, If you submit data to the browser in position format (chr#:##-##) the browser assumes this information is 1-based. If you submit data in any other format (BED (chr# ## ##) or otherwise) the browser will assume it is 0-based. You can see this both in our liftOver utility and in our search bar, by entering the same numbers in position or BED format and observing the results.
Similarly, any data returned by the browser in position format is 1-based while data returned in BED, wiggle, etc is 0-based. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Christopher Weir Maier" <[email protected]> To: [email protected] Sent: Friday, September 10, 2010 12:29:43 PM GMT -08:00 US/Canada Pacific Subject: [Genome] Question about coordinates for LiftOver: 1-based or 0-based? I realize that the coordinates presented in your internal annotation database dumps are zero-based half-open intervals. When submitting coordinates to LiftOver (specifically the web interface), is it expected that they also be zero-based, or should they be one-based? Are lifted coordinates returned as zero-based or one-based? I have not been able to find this written anywhere; the FAQ entry about this (http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1) seems only to address the browser interface and the database files, not coordinates that are user-submitted. Is the only place at all that 1-based coordinates are used the Genome Browser interface display? Thanks for the help, Christopher Maier UNC Microbiology & Immunology _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
