[maker-devel] running MAKER to merge annotations

[Arun Seetharam]

Hi Daniel,

Thanks very much for the reply!  It is the latter: same input genome under
3 settings (training was done using a different set of genes for all the
gene predictors). I simply want to get a single gff, retaining only the
best model(s) for each locus.
Are you suggesting that I can run MAKER by providing 3 files for
"maker_gff" (in maker_opts.ctl) and keeping everything else default? or do
I have to do something in the CTL file to achieve this? I appreciate if you
can provide more details for how to do this!

Thanks once again for the reply!

On Fri, Jan 1, 2016 at 12:37 PM, Daniel Ence <dence at genetics.utah.edu>
wrote:

> Hi Arun, are the three rounds of maker on different parts/versions of the
> genome or did you maker on the same genome with three different settings?
> If it’s the former, then you can merge the maker gff files with gff3_merge,
> which is included with your maker installation.
>
> If it’s the latter case then I do think EVM could help if you want to give
> the different result sets different confidence weights. If you want to give
> them all the same weight, then you could do another run of maker, and pass
> them through as either models or predictions.
>
> ~Daniel
>
>
>
>
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> > On Jan 1, 2016, at 11:31 AM, Arun Seetharam <arnstrm at gmail.com> wrote:
> >
> > Hi all,
> >
> > First of all, a very happy new year to all of you! I hope everyone is
> having a great holiday season.
> >
> > I have a question about Maker. For my grass species, I ran 3 separate
> rounds of MAKER (low GC, regular GC and high GC) and I now have 3 maker gff
> files. So, what is the correct way to merge these files to a single gff
> file? Do I have to run a maker round with just the GFF files as input? It
> looks like EVM especially meant to do this kind of job, but not sure if
> Maker does this too.
> >
> > Thanks for any help or suggestions!
> >
> > Have a nice day,
> > --
> > Arun Seetharam
> > Post Doctoral Research Associate
> > Genome Informatics Facility & EEOB
> > Office of Biotechnology
> > 228 Science I
> > Iowa State University
> > Ames, Iowa 50011
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Arun Seetharam
Post Doctoral Research Associate
Genome Informatics Facility & EEOB
Office of Biotechnology
228 Science I
Iowa State University
Ames, Iowa 50011
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