You could try our pre-compiled binaries: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Won't work if your system is too different. See also: http://hgdownload.cse.ucsc.edu/admin/exe/ for other architectures. --Hiram On 7/24/12 9:44 PM, Anton Kratz wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
