Sorry Vanessa, I managed to run it (mafsInRegion regions.bed out.maf in.maf), and fixed bed format Though I can't say it runs very fast
Many thanks, Assaf On Fri, Aug 26, 2011 at 3:49 AM, asas asasa <[email protected]> wrote: > Thanks Vanessa, > > I now installed mafsInRegion, I have a maf file downloaded from UCSC site, > and a bed file, but it is not clear how to run it. This is what the programs > says when executed with no arguments: > > 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 > > > My bed file looks like: > > chrY 4717095 4717098 + > > > > Thanks a lot, > Assaf > > On Fri, Aug 26, 2011 at 2:46 AM, Vanessa Kirkup Swing < > [email protected]> wrote: > >> Hi Assaf, >> >> Our engineer had this to say: >> >> ".lav files are only for pair-wise alignments, only two genomes. The >> MAF files have all the genomes in the multiple alignment." >> >> We recommend that you use this program: mafsInRegion which can be >> obtained from the kent source tree. Information about all of the >> utilities can be found at: >> http://genomewiki.ucsc.edu/index.php/Kent_source_utilities >> >> Information on how to obtain the source: >> http://genome.ucsc.edu/FAQ/FAQlicense.html#license3. >> >> If you have further questions, please contact the mailing list: >> [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: asas asasa <[email protected]> >> Date: Thu, Aug 25, 2011 at 4:02 PM >> Subject: [Genome] mapping the chromosomal coordinates of one species >> to other species >> To: [email protected] >> >> >> Hi all, >> >> I would like to build a script that gets start/end chromosomal coordinates >> of specific species, and rapidly finds the homologous coordinates and >> strands from other species, or to use such function/program >> if already exists (maybe in the Jim Kent's source code ?). >> But, it is important for me to get the coordinates in the maximum bp >> resolution (as the alignment include gaps, I would like to know where they >> are located). >> >> Basically, the Multiz alignments in the MAF format, store such >> information, >> but I'm wondering if there is an efficient way to extract >> this information from the files, or from similar files. In addition, >> the Multiz files are huge, and I'm looking for a more compact storage >> if exists (e.g., http://www.bx.psu.edu/miller_lab/dist/lav_format.html ). >> >> Best wishes, and thanks in advanced for any relevant help, >> Assaf >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
