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
