Infer UTRs from overlaying augustus & braker predictions with StingTie gtf

[KatharinaHoff]

We need to find someone to implement this.

[MarioStanke]

Possibly joingenes can do this: 4.2. if there is a transcript with start or stop codon in a set and a second one without this codon and they are "joinable", then this step joins the corresponding terminal exons

[vpymerel]

Hello,

First thank you very much for the software and continuous development.

Just got really nice results using braker3, at least in terms of prediction of BUSCO genes,

Second related to this issue, in the meantime, do you have an opinion on using GeMoMA annotation finalizer to add UTR to augustus.hints.gtf or braker.gtf ?

Thank you, V

[KatharinaHoff]

You can do it, but it is probably not the best way to do it, in this case. We did that before because the reads were not assembled. In braker3, you actually have the assembled transcripts that you need to infer UTRs

vpymerel @.***> schrieb am Mi. 8. März 2023 um 19:36:

Hello,

First thank you very much for the software and continuous development.

Just got really nice results using braker3, at least in terms of prediction of BUSCO genes,

Second related to this issue, in the meantime, do you have an opinion on using GeMoMA annotation finalizer to add UTR to augustus.hints.gtf or braker.gtf ?

Thank you, V

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[KatharinaHoff]

I have implemented a draft script to solve the problem of decorating our gtf files with UTRs from stringtie gff files, see https://github.com/Gaius-Augustus/BRAKER/issues/638