Dear Didion, The differences between the command line tool and the browser are explained in this FAQ:
http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 If you have further questions, please don't hesitate to contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "John Didion" <[email protected]> To: [email protected] Sent: Monday, July 19, 2010 8:47:58 AM GMT -08:00 US/Canada Pacific Subject: [Genome] liftOver inconsistencies between website and downloaded chain file I used both the website and the command line liftOver tools to map the following two positions from mm8 to mm9. The web site says that they align to exactly the same position (which is correct), whereas the command line tool says they are offset by one base pair. Why the discrepancy? Is there a more up-to-date chain file that I need to get? chr2:175394423-175394447 chr2:175025341-175025365 -- John Didion Computational Biology, PhD Student Fernando Pardo-Manuel de Villena Lab UNC Chapel Hill _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
