Hello, Vlad. When performing a liftOver, there is a minimum number of bases that must remap for a successful liftOver. You can control the number of remapped bases required for a successful liftOver by changing the "Minimum ratio of bases that must remap" setting in the liftOver tool. By default, this setting has a value of 0.95 (95%). When you specified only two bases in your liftOver, it met the minimum 95% value, but when you specified the entire range, only approximately 90% of the bases remapped. If you change this setting to 0.9 (90%), your liftOver will be successful.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Vladmir Makarov Sent: Tuesday, February 21, 2012 6:51 PM To: [email protected] Subject: [Genome] liftOver tool error from HG18 to HG19 Hello, I was trying to convert coordinates with http://genome.ucsc.edu/cgi-bin/hgLiftOver chr1:144,112,610-144,639,480 from HG18 to HG19 but getting error message: #Partially deleted in new However, when I convert the coordinates separately (chr1:144,112,610-144,112,611 and chr1:144,639,480-144,639,481) it works. I can view the new hg19 coordinates in genome browser (chr1:145,401,254-145,928,124) What would be the reason? -- Many thanks and best wishes, Vlad _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
