Hello, The liftOver files are based on the Chain track results (same process creates them all at once). So, both assemblies would need to be in a UCSC database (could be your own mirror, where you create the missing assembly).
If the underlying assembly changed significantly, then less data will lift, regardless of the track. A work-around would be if you were willing to tune the parameters and do multiple cycles of analysis (this is actually less difficult than it may originally sound, but it does take some time to do and will not resolve every case. There are just no pre-set parameters that produce the best results for all cases.) BLAT would always be a good tool for re-alignment of sequence data. Here is a link to the source code: http://genome.ucsc.edu/FAQ/FAQdownloads#download27 Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Nicolas Berbenetz" <[email protected]> wrote: > From: "Nicolas Berbenetz" <[email protected]> > To: [email protected] > Sent: Thursday, September 10, 2009 1:18:12 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] S. cerevisiae liftover data for builds Oct-2003 to Feb-2006 > > Hi, > > > > Is there a script available to generate LiftOver files? I'm interested > in > converting coordinates between the Oct-2003 SGD build on the USCS > website to > a Feb-2006 SGD build. > > Or is the best way to convert between genome assemblies to perform a > BLAT > search? > > > > Regards, > > Nick > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
