Dear UCSC team, Hiram, > With these MAF files, a bed file of your specific regions and the kent program mafsInRegion
Where can I get source or binary for mafsInRegion? I think I found it's source in the UCSC genome browser source ( http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)? But according to README.building.source I would have to build the entire thing locally? It's a bit tough... (steps 3a - 5 are a bit complex, and I cannot / don't want to build mySQL on the intended target machine). Is there a more direct way to get the source for mafsInRegion and compile only this one? Thanks. Anton On Fri, Jul 20, 2012 at 3:01 PM, Hiram Clawson <[email protected]> wrote: > Good Evening Anton: > > You can fetch a beta release set of MAF files for a 60-species alignment > on Mouse/GRCm38/mm10 from our test server: > > http://hgdownload-test.cse.**ucsc.edu/goldenPath/mm10/**multiz60way/maf/<http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/multiz60way/maf/> > > Or the 46 species alignment MAF files from Human/GRCh37/hg19: > http://hgdownload.cse.ucsc.**edu/goldenPath/hg19/**multiz46way/maf/<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/> > > Beware, these are gigantic files. With these MAF files, a bed file > of your specific regions and the kent program mafsInRegion, you can > obtain the sequence out of these files. It is not perfectly in multi Fasta > format, but it is close enough for a simple transformation. > > --Hiram > > mafsInRegion - Extract MAFS in a genomic region >> usage: >> mafsInRegion regions.bed out.maf|outDir in.maf(s) >> options: >> -outDir - output separate files named by bed name field to outDir >> -keepInitialGaps - keep alignment columns at the beginning and of a >> block that are gapped in all species >> > > On 7/19/12 10:07 PM, Anton Kratz wrote: > >> Dear UCSC team, >> >> I have a list of a couple of thousand exons or regions on the rat (rn4) >> genome defined as start-end coordinates in bed format. These regions are >> not in RefSeq, RGD or elsewhere, they are novel determined by me. I want >> to >> check for coding/noncoding poteintial with phyloCSF ( >> https://github.com/mlin/**PhyloCSF/wiki/<https://github.com/mlin/PhyloCSF/wiki/> >> ). >> >> Is there any way how I programmatically can get multi-genome alignment for >> my regions, in FASTA-format? Ideally for the 29 mammals phylogeny but any >> other multi-alignment containing mammals is fine too. >> >> I was searching around in the data at UCSC provided in context of the 29 >> mammals >> (http://genomewiki.cse.ucsc.**edu/index.php/29mammals<http://genomewiki.cse.ucsc.edu/index.php/29mammals>) >> project, but >> can't find the actual multi-fasta alignment. >> >> Thanks. >> >> Anton >> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
