Hello, The mm4 database in archived, but the data is still available. Also, the lift will need to be done in two steps. You will need to ftp both files and the executable liftOver (if you do not already have it).
Ftp instructions: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 To find the starting file, ftp to the genome-archive.cse.ucsc.edu server (instead of hgdownload.cse.ucsc.edu) and find the data at this path: goldenPath/mm4/liftOver/mm4ToMm7.over.chain.gz To find the next file, ftp to the regular location hgdownload.cse.ucsc.edu and find the data at this path: goldenPath/mm7/liftOver/mm7ToMm8.over.chain.gz I was able to locate the archived data (and server/path) by looking at the mouse section on the Downloads page (scroll to bottom of mouse section to find this link: Archived mm4 liftOver files). The server name and path in the url from the Downloads area can be used to locate files for ftp. The very last section of the Downloads page has a section called "LiftOver Files (over.chain)" that has links/info for liftOver executable. The regular web hgLiftOver tool already also has the Mouse Oct. 2003 (mm4) archived liftOver and Mouse Aug. 2005 (mm7) liftOver files ready to use through the Browser (for smaller datasets). Hope this helps, please let us know if you need more assistance, Jennifer Jackson UCSC Genome Bioinformatics Group Ilana Livyatan wrote: > Hello, > I would like to convert coordinates from mus musculus mm4 (build 32) to mm8 > using liftOver. I do not see the required over.chain file on the site and > would like to request it. > > Thanks, > Ilana Livyatan > Eran Meshorer Lab > Hebrew University > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
