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 -- Dr Conrad Nieduszynski BBSRC David Phillips Fellow Institute of Genetics, School of Biology, The University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH UK This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
