[maker-devel] repeat statistics

[Jason Stajich]

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
>
>
>
>
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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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>
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