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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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add transcriptomes to input #812

Closed YanisChrys closed 2 months ago

YanisChrys commented 2 months ago

Hello,

I am using published annotations of closely related species to annotate my genomes and they provide of course with the transcriptomes produced during their experiments. (*rna.faa.gz files) and arguably these are good assembled gene transcripts that also incude UTRs.

Is there a way to use these with BRAKER? Is there a benefit in using these together with the protein sequences they are used to create? Finally, if not, may I suggest including the possibility of including this data in BRAKER?

This could be related to the following issue:

https://github.com/Gaius-Augustus/BRAKER/issues/585

KatharinaHoff commented 2 months ago

There are lot of ideas and no manpower to implement things at the moment.

You can use transcriptome evidence of this type in WebAUGUSTUS.

YanisChrys commented 2 months ago

That's understandable, but thank you for replying and thank you for the suggestion! :)