Hello, Here are a few links to some help documents to create this type of file. More is in the README files in the kent source tree. The basic idea to create a chain file between two genomes (the process makes an over.chain file at the same time). Reading the track description in the Assembly browser for Chains is also recommended, as it has Methods, Credits, and links to external tools or related publications.
http://genomewiki.ucsc.edu/index.php/Chains_Nets http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver http://genomewiki.cse.ucsc.edu/index.php/The_source_tree http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities http://genome.ucsc.edu/FAQ/FAQdownloads#download27 http://genomewiki.cse.ucsc.edu/index.php/Category:Technical_FAQ Please review and let us know if you have any questions, Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "jdidion" <[email protected]> wrote: > From: "jdidion" <[email protected]> > To: [email protected] > Sent: Wednesday, January 13, 2010 2:55:34 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] how to create over.chain files? > > I have used the snp and indel data released by the sanger mouse > genomes > project to impute the genomes of the 17 strains being sequenced. Now I > want > to map genomic positions between the reference genome and any of the > 17 > imputed genomes. How do I create an over.chain file so that I can do > this > with the liftover tool? > > Thanks! > > John Didion > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
