Explanation for fix_in_frame_stop_codon_genes.py

[LeebanY]

Hi all,

I was wondering how augustus distinguishes between internal stop codons that represent 'true' pseudogenization as opposed to something going wrong with characterising the boundaries of genes? If, for example, internal stop codons in the 'bad_genes.lst' file were replicated in other closely-related genomes that were trained on independent RNA-seq, is that an indication of something biologically interesting, or is it always a case of difficulty determining gene structure (that needs to be fixed by the script)? And does the script always 'fix' internal stop codons, or is it the case that sometimes the script determines that these internal stop codons are 'real'?

Thanks!

Leeban

[KatharinaHoff]

There is no magic here... it’s only detection of predicted in frame stop codons. They are predicted because Augustus doesn’t see them when they are spliced. This has nothing to do with pseudogenes.

Best,

Katharina

On Fri 18. Sep 2020 at 16:07, LeebanY [email protected] wrote:

Hi all,

I was wondering how augustus distinguishes between internal stop codons that represent 'true' pseudogenization as opposed to something going wrong with characterising the boundaries of genes? If, for example, internal stop codons in the 'bad_genes.lst' file were replicated in other closely-related genomes that were trained on independent RNA-seq, is that an indication of something biologically interesting, or is it always a case of difficulty determining gene structure (that needs to be fixed by the script)? And does the script always 'fix' internal stop codons, or is it the case that sometimes the script determines that these internal stop codons are 'real'?

Thanks!

Leeban

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[LeebanY]

That makes sense. Thanks!

[XK4959]

Creating directory tmp_jkulsosc/. Error in file /users/gaoxl/soft/miniconda3/bin/fix_in_frame_stop_codon_genes.py at line 225: /users/gaoxl/soft/Augustus-3.3.1-tag1/scripts/gtf2gff.pl is not executable!

[KatharinaHoff]

This seems to be a copy of https://github.com/Gaius-Augustus/Augustus/issues/248

On Mon, Jan 4, 2021 at 6:56 AM Jarhan [email protected] wrote:

Creating directory tmp_jkulsosc/. Error in file /users/gaoxl/soft/miniconda3/bin/fix_in_frame_stop_codon_genes.py at line 225: /users/gaoxl/soft/Augustus-3.3.1-tag1/scripts/gtf2gff.pl is not executable!

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