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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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Restricting introns to RNA seq support #787

Open allind opened 3 months ago

allind commented 3 months ago

Hi, is it possible to stringently require all introns considered by braker to have support in the RNA-seq data provided? I am finding that braker is adding a lot of introns to gene predictions that are not supported by the RNA data and are likely erroneous. I'm working with an organism where introns are relatively rare. Thanks!

KatharinaHoff commented 3 months ago

Maybe a custom strategy could help you. Imagine running two gene finders: one that predicts only intron-less genes, and one that predicts genes with introns (such as BRAKER). Then combine the intron-less genes with the intron-supported genes. The last step can be performed with TSEBRA. Just an idea.