[maker-devel] repeat statistics

[Barry Moore]

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
> 
> From: Jason Stajich <jason.stajich at gmail.com>
> Date: Monday, April 29, 2013 5:49 PM
> To: Barry Moore <barry.moore at genetics.utah.edu>
> Cc: Eric Ross <ejr at stowers.org>, "maker-devel at yandell-lab.org" <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 SOBA
> 
> 
> Jason Stajich
> jason at bioperl.org
> 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> 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
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
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>> maker-devel at box290.bluehost.com
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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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