[Genome] [Fwd: Re: Multiz maf, ftp and intersection]

[Brooke Rhead]

Hi again Jimmie,

I forgot to mention that the 17-way MAF alignment files for hg18 are 
available on our downloads server, here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz17way/

--
Brooke Rhead
UCSC Genome Bioinformatics Group


-------- Original Message --------
Subject: Re: [Genome] Multiz maf, ftp and intersection
Date: Tue, 08 Apr 2008 10:52:22 -0700
From: Brooke Rhead <rhead at soe.ucsc.edu>
To: Ye, Jimmie <jimmie.ye at amylin.com>
CC: genome at soe.ucsc.edu
References: <3BAB685D43723A4EA756F7F415A5BD21A1FCB7 at A-EXCH-VS1.amylin.com>

Hello Jimmie,

There is not a way to obtain sequence from our MySQL server, as the
sequence is stored only in the MAF file, not in a table.

If you want to work with MAF files at the command line, there are some
tools in the Genome Browser source tree for working with MAFs,
(http://genomewiki.ucsc.edu/index.php/Kent_source_utilities -- search
for "maf").  You can download the source from:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Run any command with no arguments to see a usage statement.  For example:

$ mafsInRegion
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

Another option for working with MAFs is the Galaxy website,
http://main.g2.bx.psu.edu/ .  Galaxy is run by Penn State but works in
conjunction with the UCSC Genome Browser.  Look under the "Fetch
Alignments" header on the left-hand side of the page for several tools
for working with MAFs.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Ye, Jimmie wrote:
> Hi,
> 
> I'm interested in obtaining maf alignments in bulk but I need to be able
> to intersect the output of multiz17way with the list of known genes like
> the option that's available under the table browser...how can I do this
> in mysql?  Can someone from UCSC perhaps post a sample query in sql?
> 
> Thanks
> 
> ~Jimmie
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
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