Maker yields sequences without start and stop codon

[Emmanuel Nnadi]

Hi Carson

I always set always_complete=1 yet I still get sequences without start and stop codon. 

Can https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py be used on the final sequence to fix start and stop codon problem?

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[Carson Holt-2]

Maybe. I’ve never tried it. MAKER just wanders upstream and downstream, then gives up if it doesn’t find anything to add. Perhaps this script does something similar. If it takes GFF3, may be worth a shot.

—Carson

On Oct 27, 2020, at 9:01 PM, Emmanuel Nnadi <[hidden email]> wrote:

Hi Carson

I always set always_complete=1 yet I still get sequences without start and stop codon. 

Can https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py be used on the final sequence to fix start and stop codon problem?

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