----- Original Message ----- From: "Jennifer Jackson" <[email protected]> To: "Otis Harrison" <[email protected]> Sent: Tuesday, July 21, 2009 10:22:15 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Hi, I had a question about liftover
Hello, The liftOver program uses a mapping file derived from the "Chain track" process. Please see that track for exact processing details. To run liftOver, there is a web version and a line command version. Try using the default parameters to start with (in the web version these are described for same=species as minMatch=0.90 and multiple=N). The usage for the line command can be found by typing the program in at a unix prompt without any arguments. Very often it is necessary to adjust the parameters for regions that fail liftOver with the strict defaults. http://genome.ucsc.edu/cgi-bin/hgLiftOver LiftOver files (chain.over) are located in the "from" species location on Downloads. Browse to species, enter the LiftOver directory to view file names/paths. The, ues ftp to retrieve files. The other input is the data you wish to map (several formats excepted, BED is the easiest) and the output is generated by the program (mapped and unmapped). Please let us know if you need help once started, Jennifer Jackson UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Otis Harrison" <[email protected]> To: [email protected] Sent: Tuesday, July 21, 2009 8:57:06 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Hi, I had a question about liftover > Hi you doing, I was trying to find any documentation about liftover > and wondering if you might have any documentation. I am new to > bioinformation and I am trying to learn how to align an old version > cow with a new version of cow. And just how the liftover program > does this. > > Thank you so much for any help you can give. > Otis _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
