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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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In braker annotation what are sequence ids start with jg, g and m1-g? #726

Closed mudithekanayake closed 11 months ago

mudithekanayake commented 11 months ago

Hi, I have annotated a genome and I have the gtf file. Most of the ids start with jg but there are few sequence ids which start with g and m1-g. I tried find what they are but I could not. Can someone explain why there are differences like that in the gtf file. Thank you.

KatharinaHoff commented 11 months ago

The question indicates that you are using a very old version of BRAKER. Please update BRAKER.

The different name stems of genes in that old version indicate the origin of the gene structure. The current BRAKER unifies names (and also merges the transcript sets differently and better.)