[maker-devel] repeat statistics

[Ross, Eric]

Works now.

Thanks much,

Eric
--
Eric Ross
Bioinformatic Specialist I
Alejandro Sánchez Alvarado Laboratory
Stowers Institute for Medical Research
Howard Hughes Medical Institute
ejr at stowers.org

From: Barry Moore <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>
Date: Wednesday, May 1, 2013 6:42 PM
To: Eric Ross <ejr at stowers.org<mailto:ejr at stowers.org>>
Cc: Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] repeat statistics

Eric,

Try again,  it should have been world readable before, but I've opened it a bit wider now, so should definitely be now.  Let me know if you have problems.

B

On May 1, 2013, at 9:57 AM, Ross, Eric wrote:

Should this be accessible anonymously?

I'm unable to connect.

Eric


--
Eric Ross
Bioinformatic Specialist I
Alejandro Sánchez Alvarado Laboratory
Stowers Institute for Medical Research
Howard Hughes Medical Institute
ejr at stowers.org<mailto:ejr at stowers.org>

From: Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>
Date: Monday, April 29, 2013 5:49 PM
To: Barry Moore <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>
Cc: Eric Ross <ejr at stowers.org<mailto:ejr at stowers.org>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] repeat statistics

Barry - I think you mean topaz instead of malachite?

svn co svn://topaz.genetics.utah.edu/SOBA/trunk<http://topaz.genetics.utah.edu/SOBA/trunk> SOBA


Jason Stajich
jason at bioperl.org<mailto:jason at bioperl.org>
jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>
http://bioperl.org/wiki/User:Jason
http://twitter.com/hyphaltip


On Mon, Apr 29, 2013 at 10:59 AM, Barry Moore <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>> wrote:
Hi Eric,

There is a command line version of SOBA.  It does the same things as the web version and much more.  This page has some basic details:

http://www.sequenceontology.org/resources/sobacl.html

Ultimately you'll get it like this:

svn co svn://malachite.genetics.utah.edu/SOBA/trunk SOBA

Then run:

SOBA/bin/SOBAcl --help

For a lot of command line examples have a look in:

SOBA/t/sobacl_test.sh

B

On Apr 29, 2013, at 9:58 AM, Ross, Eric wrote:

Does anyone have a good tool for yanking repeat statistics out of MAKER
gff files?

SOBA can give some basic stats, but it doesn't play well with my giant
files and I haven't figured out a way to run it locally.

For that matter does anyone have a script that will calculate SOBA like
stats locally?  I'd rather avoid writing one myself if something else is
out there.

Thanks,

Eric

--
Eric Ross
Bioinformatic Specialist I
Alejandro Sánchez Alvarado Laboratory
Stowers Institute for Medical Research
Howard Hughes Medical Institute
ejr at stowers.org<mailto:ejr at stowers.org>




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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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