[maker-devel] repeat statistics

[Barry Moore]

Let me know how it works out for you - feedback either positive or negative is useful.

B

On May 1, 2013, at 5:53 PM, Ross, Eric wrote:

> 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>
> Date: Wednesday, May 1, 2013 6:42 PM
> To: Eric Ross <ejr at stowers.org>
> Cc: Jason Stajich <jason.stajich at gmail.com>, "maker-devel at yandell-lab.org" <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
>> 
>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> 

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




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