Hi Martin, I'm sorry, but we do not have the tools here to do that. I looked at the Galaxy website (http://main.g2.bx.psu.edu/), and some of their tools may be of use to you, particularly those under the "Fetch Alignments" section. If you have questions about Galaxy, please contact their help desk at [email protected] <mailto:[email protected]>.
Additionally, one of our engineers suggested using a multiple aligner like multiz, pecan, or TBA. He also noted that "MAF files are only guaranteed to be single coverage on the reference, so there can be sequence from the other species that appears more than once aligned to different regions of the reference genome. One can't just reorder by the other species' coordinates and expect to get single coverage on the new reference." I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/11/10 6:51 PM, Martin Smith wrote: > Greeting everyone, > > Would anyone have an idea if some tool exists that sorts (and > potentially reverse complements) a maf file based on chromosomal > coordinates of the unsorted reference species? > > Cheers, > > Martin > > On 12/08/2010, at 11:48 AM, Martin A. Smith wrote: > > >> G'day Jennifer, >> >> Thanks for your consideration. I am familiar with mafOrder; it >> changes the order of species in the alignments. To my knowledge it >> does not sort and, when required, reverse complement the output. You >> see, I would like to use the re-ordered maf file as input for >> hgLoadMaf, which requires a sorted (i.e. corectly ordered) maf file >> in + orientation as input. >> >> Cheers, >> >> Martin >> >> On 11/08/2010, at 4:57 AM, Jennifer Jackson wrote: >> >> >>> Hello Martin, >>> >>> There is a utility in the kent source tree that you can use to re- >>> order a maf file: >>> >>> $ mafOrder >>> mafOrder - order components within a maf file >>> usage: >>> mafOrder mafIn order.lst mafOut >>> where order.lst has one species per line >>> >>> How to get the kent source tree: >>> http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads >>> >>> Please feel free to contact the mailing list support team again if >>> you would like more assistance. >>> >>> Warm regards, >>> >>> Jen >>> UCSC Genome Browser Support >>> >>> On 8/10/10 12:04 AM, Martin A. Smith wrote: >>> >>>> Esteemed colleagues, >>>> >>>> I was wondering if there is an existing tool that sorts a group of >>>> maf >>>> blocks with respect to some specie's coordinates. In other words, I >>>> would like to reorder a MSA with reference species X to reference >>>> species Y and upload it as a custom track for database Y. >>>> >>>> Kind regards, >>>> >>>> Martin Smith >>>> PhD Student >>>> Institute for Molecular Bioscience >>>> University of Queensland >>>> _______________________________________________ >>>> 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
