I've tested Braker2 using RNAseq on a non-model organism, and it does a terrible job. The main problem is the intron prediction.
Training Augustus for Gene Prediction
I am working on a plant genome and have a genome FASTA file. I also have GenBank file containing some manually curated reference gene models from a previous genome version. My species is not available in the Augustus species folder. How can I use both datasets (genome + genbank gene models) to train Augustus using augustus itself or may be using BUSCO and perform gene prediction effectively?
Thanks in advance!!
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GALBA can help you to train Augustus models on your genome https://github.com/Gaius-Augustus/GALBA?tab=readme-ov-file#what-is-galba
That said, the authors recommend BRAKER3 if you have RNA-seq.
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