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
>
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