Inconsistencies in gene IDs in the file created Augustus.hints.aa

[minhasbushra]

Hi,

I am using the most current version of braker and just noticed some inconsistencies in the gene IDs. Some are starting with "jg" and others with "g". In the gtf file I don't see the ones starting with g (the only point where I find that ID is in the message here "This transcript jg16134.t1 is derived from g29739.t1 from the input file /***/braker_ETP/augustus.E.gtf"). But they have a protein sequence in the Augustus.hints.aa file.

Please let me know what if any is the difference between these two IDs.

Thanks Bushra

[tomasbruna]

Hi Bushra,

I guess you are using BRAKER in the "ETP" mode. There are indeed some known issues with the gene IDs in this mode. I'd suggest using the newly developed TSEBRA tool to combine RNA-Seq and proteins with BRAKER. It will fix these ID issues, and, more importantly, should lead to better results.

Best, Toams