[maker-devel] Augustus predictions within MAKER2

[Jason Stajich]

I’d check the documentation and the raw files in the run folder if you
aren’t sure but The maker consensus models will have maker in the 2nd
column and the augustus will have augustus in second  column of gff
(‘source’)

You might need to adjust your grep to only take those with augustus in 2nd
Col. you can do grep -P “\taugustus\t” to get those.


On Fri, Nov 25, 2022 at 8:56 AM Alam,Elissa <elissaralam at ufl.edu> wrote:

> Would that include all the gene models predicted by Augustus or only the
> ones that Maker retains after considering all ab initio gene predictions
> (SNAP + Augustus) and the EST evidence?
>
>
>
> Thanks a lot,
>
> Elissar
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
>
>
>
> *From: *Jason Stajich <jason.stajich at gmail.com>
> *Sent: *Friday, November 25, 2022 11:51 AM
> *To: *Alam,Elissar <elissaralam at ufl.edu>
> *Cc: *maker-devel at yandell-lab.org
> *Subject: *Re: [maker-devel] Augustus predictions within MAKER2
>
>
>
> *[External Email]*
>
> After you run the gff3_merge step you can
>
> grep augustus final.gff > augustus.gff3
>
>
>
> On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <elissaralam at ufl.edu> wrote:
>
> Hello,
>
>
>
> I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I
> would like to use the gene predictions generated by Augustus (prior to
> MAKER selecting the final gene model based on all ab initio predictions)
> for downstream analyses. Is there a way to obtain the Augustus gene
> predictions in gff3 format from MAKER2?
>
>
>
> Thanks a million,
>
> Elissar
>
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> --
>
> Jason Stajich
> jason.stajich at gmail.com
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>
>
-- 
Jason Stajich
jason.stajich at gmail.com
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