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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Braker3 gff3 output #617

Closed RenscoHogers closed 1 year ago

RenscoHogers commented 1 year ago

Hello,

I have been able to run braker3 successfully, however, the braker3.gff3 output seems a bit off. There is not a single "gene" feature in the entire .gff3, I have checked the Augustus.hints.gtf file and that one does include "gene" features. Is there a reason why these are left out of the braker3.gff3 file?

It seems to be that all gene annotations found in the augustus hint file, are placed in the braker.unsupported.gtf file, namely 22 373/23 914. Where the remaining gene feature are, I do not know,

I would like to combine the braker.gff3 file with GenomeThreader and transdecoder using evidencemodeler, and to me it seems that the gene features are needed. Any thoughts?

Thanks in advance!

LarsGab commented 1 year ago

Hi,

this should be fixed in BRAKER v3.0.3

Best, Lars