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

[Felipe Barreto]

Awesome!  Thanks for the tips and script.  This should do the trick.  Will
come back if I get stuck.

Felipe


On Wed, May 28, 2014 at 11:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Felipe Barreto
Post-doctoral Scholar
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140528/55f8002a/attachment-0003.html>