Hello, Many times the liftOver files are created in pairs, however not for this case. The program works equally well forwards or backwards for line command and the web browser. The over.chain file is always located in the "from" assembly's data on Downloads. Sometimes, a few cycles are necessary - we have found no problems with doing this for the vast majority of data (especially same species lifts, with more "finished genomic", such as human). A few spot checks using Blat can help you to confirm that the results are what you expect.
For March 2006->July2003 the ftp files for the line command are located here (two lifts required hg18-> h17 + hg17-> hg16) http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ -> hg18ToHg17.over.chain.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg17/liftOver/ -> hg17ToHg16.over.chain.gz Consider the web versions if your data set is smaller 1) batches: http://genome.ucsc.edu/cgi-bin/hgLiftOver 2) single location: Assembly browser (from database), click on Convert in top blue bar. Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Hannah Watkins" <[email protected]> To: "genome" <[email protected]> Sent: Tuesday, July 21, 2009 10:06:50 AM GMT -08:00 US/Canada Pacific Subject: [Genome] backwards liftover Hi, I have a set of coordinates from the human genome March 2006 assembly that I am trying to liftover backwards to find out where they would have been in the human genome July 2003 assembly. The regular liftover only allows you to go forwards. Do you have any suggestions? Thanks, Hannah Watkins _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
