Hi Shan, This was a bit tricky to find!
~kent/src/hg/ratStuff/mafSpeciesSubset/ I used this file to locate the source: ~kent/src/sources Thanks, Jen On 3/24/10 10:06 PM, 董珊 wrote: > > > ---------- 已转发邮件 ---------- > 发件人： *董珊* <[email protected] <mailto:[email protected]>> > 日期： 2010年3月24日 下午3:03 > 主题： Re: [Genome] Create multiple alignment of 12 Drosophila species > genomes > 收件人： Jennifer Jackson <[email protected] <mailto:[email protected]>> > > > Hello Jennifer, > > There is a problem when I get the mafSpeciesSubset program. > I have already follow the guide "Source tree compilation on > Debian/Ubuntu" and the guide in > _http://genome.ucsc.edu/admin/jk-install.html__._ > But there is no "mafSpeciesSubset" in the kent/src/*. > I don't know why. > > > Thank you very much in advance! > > Shan > > > 2010/3/23 Jennifer Jackson <[email protected] <mailto:[email protected]>> > > Hello, > > The utility mafFilter is the best choice: use option -speciesFilter. > You do not need to set up the entire code tree or a mirror to use > the utilities in the kent source tree. > > http://genomewiki.ucsc.edu/index.php/The_source_tree > http://hgdownload.cse.ucsc.edu/downloads.html -> Source > > mafFilter - Filter out maf files. Output goes to standard out > usage: > mafFilter file(s).maf > options: > -tolerate - Just ignore bad input rather than aborting. > -minCol=N - Filter out blocks with fewer than N columns (default 1) > -minRow=N - Filter out blocks with fewer than N rows (default 2) > -factor - Filter out scores below -minFactor * (ncol**2) * nrow > -minFactor=N - Factor to use with -minFactor (default 5) > -minScore=N - Minimum allowed score (alternative to -minFactor) > -reject=filename - Save rejected blocks in filename > -needComp=species - all alignments must have species as one of the > component > -overlap - Reject overlapping blocks in reference (assumes ordered > blocks) > -componentFilter=filename - Filter out blocks without a component > listed in filename > *-speciesFilter=filename* - Filter out blocks without a species > listed in filename > > Hopefully this helps, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > > On 3/22/10 1:42 AM, 董珊 wrote: > > Dear Genome list, > > I want to ask a question about creat a multiple alignment from > pair-wise > alignments from UCSC Genome Blowser. > The whole genome multiple alignment I need is from 12 Drosophila > species, > but the multiple alignment data on UCSC Genome Blowser contain 3 > excess > species (A. gambiae, A. mellifera and T. castaneum). > > I know there is a complex method to use multiz/TBA to get > multiple alignment > from pair-wise alignments. > However, these pair-wise alignments must in MAF format. > But it seems difficult to get the format convert tool on Kent > source. > Do you know other method to remove the 3 excess species from the > multiple > alignment from UCSC Genome Blowser? > > Thank you very much in advance! > > Best regards! > Shan > _______________________________________________ > Genome maillist - [email protected] > <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
