[maker-devel] Maker annotation result contain 10% of gene with incorrect start or stop codon

[Jacques Dainat]

Hi,

I met this problem in some projects where the ORFs were not well defined. In the mRNA it was not the longest ORF chosen, which is not necessarily wrong but here it was obviously not the correct one chosen. Probably due to bad training of my abinitio tools. 
I ended up to develop a script to fix the predictions and use the longest ORF as CDS. The script is  called agat_sp_fix_longest_ORF.pl <https://github.com/NBISweden/AGAT/blob/master/bin/agat_sp_fix_longest_ORF.pl> 
It is available within AGAT (https://github.com/NBISweden/AGAT)

Hoping it could help,

Best regards,

Jacques Dainat, Ph.D.


> On 8 Mar 2021, at 11:25, 廖家緯 <jwliao25 at gmail.com> wrote:
> 
> Hi maker-devel group,
> 
> I used the maker with SNAP and Augustus for annotating a green algae genome. I always set the 'always_complete=1'  from the first round of annotation.
> 
> After Augustus training, I still get around 1111 and 208 genes that don't have the correct start and stop codon. (Total annotated gene number is 12696)
> 
> I provided the close species proteome and the green algae its own RNA-seq data for EST hint.
> 
> Does that make sense? Does there have any way to improve the result or fix the incorrect start and stop codon for those gene?
> 
> best,
> Chai-Wei Liao
> 
> --------------------------------------------------
> 
> Chia-Wei Liao 廖家緯
> 
> Research Assistant
> 
> Institute of Molecular Biology,
> 
> Academia Sinica, Taipei City, Taiwan
> 
> Phone: 886-2-2789-9216 (Lab)
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20210325/4c12809e/attachment-0003.html>