Hello YU, Use the liftOver utility to transform the data. This is in the kent source code, but also available pre-compiled for several platforms.
You may also want to review the web version of the tool to note the parameters we use for same-species lifts (most are default). From the downloads page, scroll down to "Source Downloads -> LiftOver tool" and follow the links. http://hgdownload.cse.ucsc.edu/downloads.html The usage for the program (type program at prompt without any arguments) explains the inputs. One of these is the appropriate over.chain file. For your case, hg18->hg19, the file is called hg18ToHg19.over.chain.gz and is located here for ftp: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ If you need any help once you get started, please feel free to write back to the mailing list for more help. The mailing list archives also contain many questions w/ answers for liftOver-related topics. Search from this page: http://genome.ucsc.edu/contacts.html -> "Search the Genome mailing list archives:" Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/26/10 2:55 PM, Yuan Jian wrote: > hi ucsc genome, > > I have BED file generated from hg18, how can I change it to hg19-based? > > thanks > YU > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
