Hello, I have an update for you. The program "mafFrag" along with a BED6 file that includes the strand set as (-) will produce a reverse complimented MAF.
Other tools such as "mafFrags" and the one you mention do not reverse-compliment currently and are under review. I hope this is helpful. We appreciate you input and hope to clarify the usage scope of the other tools in the near future, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Martin Smith" <[email protected]> > Cc: [email protected] > Sent: Tuesday, December 8, 2009 3:46:07 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] mafsInRegion doesn't reverse-complement > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
