[maker-devel] Augustus predictions within MAKER2

[Alam,Elissar]

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

[Jason Stajich]

After you run the gff3_merge step you can 

grep augustus final.gff > augustus.gff3 

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Jason Stajich
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[Alam,Elissar]

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 for Windows

 

From: Jason Stajich
Sent: Friday, November 25, 2022 11:51 AM
To: Alam,Elissar
Cc: maker...@yandell-lab.org
Subject: Re: [maker-devel] Augustus predictions within MAKER2

 

[External Email]

[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. 

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Jason Stajich
jason....@gmail.com