Hello, All genomic alignments are stored in the forward genome orientation. There are tools to reverse complement (faRc) if there are regions that you want to convert. All of the maf utilities are described here (do a "find" on maf): http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities
And here is some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Martin Smith" <[email protected]> wrote: > From: "Martin Smith" <[email protected]> > To: [email protected] > Sent: Wednesday, November 25, 2009 8:18:12 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] mafsInRegion doesn't reverse-complement > > G'day all, > > I hope I am sending this to the right place. > I just came across a pretty serious shortcoming of the mafsInRegion > script: apparently, the tool doesn't reverse-complement the alignments > > from bed file entries with (-) orientations. > > Thanks for your consideration. > > Martin A. Smith, M.Sc > ============== > PhD candidate > Mattick Group > Institute for Molecular Bioscience > University of Queensland > Brisbane, Australia > Ph: +07 3346 2075 > [email protected] > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
