[maker-devel] Adding non-overlapping models to final set

[Carson Holt]

For convenience you can use the attached script to help pull out the
match/match_part features you want from the GFF3 file (or you can pull them
out yourself).  Then do just like Daniel said by setting keep_preds=1 and
giving the selected match/match_part features to pred_gf, and your current
MAKER models to model_gff.

--Carson



From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Wednesday, May 28, 2014 at 12:35 PM
To:  Felipe Barreto <fbarreto at ucsd.edu>
Cc:  MAKER group <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Adding non-overlapping models to final set

Hi Felipe, I'm glad to hear that you got some more genes from IPRscan. If
you don't care about getting the functional information from the IPRscan
report and into the gff file, then you just need to pull those predictions
out from all the ab-initio predictions that you don't care about and put
them in a fasta file. Then you put that file in for the "pred_gff" option
and set keep_preds=1. That will promote those predictions to full gene
models. Then you can merge with your other gff3 file.

~Daniel



Daniel Ence
Graduate Student
dence at genetics.utah.edu
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On May 28, 2014, at 11:39 AM, Felipe Barreto <fbarreto at ucsd.edu>
 wrote:

> Hi, all, 
> 
> I finished generating Maker gene models.  Following suggestions here and from
> publications, I used IPRscan on the set of non-ovelapping ab initio protein
> models.  This identified ~200 models with protein domains, and I would like to
> add those to my final gene set.
> 
> However, I am having trouble figuring out how to use Maker's options to update
> my final maker_genome.gff file to include these 200 models, without also
> adding the remaining ~8000 non-overlapping models I don't want.   The
> discussions about the re-annotation options don't seem to get at this.
> 
> Do I have to first find a way to create a new gff file containing only the 200
> new models, and then simply use gff3_merge with the full genome gff?
> 
> At this point, I am not concerned about incorporating IPRscan functional info
> into the gff file.  I want simply to generate an updated (and final) gene set
> and then move on to functional annotation.
> 
> 
> Thanks yet again!
> 
> Felipe
> 
> 
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