Hello Conrad, UCSC does not have the liftOver file for the additional yeast genome. The genome itself is not even a part of the UCSC dataset.
You are correct in thinking that the implementation would be non-trivial, however using a MAC is not an issue (the genomes are small). For the environment set up, start with kent/src/README Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/24/10 3:10 AM, Conrad Nieduszynski wrote: > Hi, > > I have been using the command-line version of the liftOver tool on MacOSX to > convert between assemblies of the S. cerevisiae genome. At present UCSC only > has two assemblies (sacCer1: Oct2003 and sacCer2: Jun2008). I would like to > convert between other assemblies (specifically Jan2006) and to do this > requires the appropriate over-chain files. I have read the 'Minimal Steps For > LiftOver' page on the wiki > (http://genomewiki.cse.ucsc.edu/index.php/Minimal_Steps_For_LiftOver) and the > more detailed instructions (/kent/src/hg/doc/liftOver.txt), but implementing > this on MacOSX does not look trivial. Are additional over-chain files > available? Alternatively are there instructions for running > doSameSpeciesLiftOver.pl and for installing the required dependencies? > > Many thanks for any help you can offer, > > Conrad > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
