---------- 已转发邮件 ---------- 发件人： 董珊 <[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]>
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]> 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] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
