Hi Steve That is helpful, Thank you for your response Vlad 2012/2/23 Steve Heitner <[email protected]>: > 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 >
-- Many thanks and best wishes, Vlad _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
