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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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Many gene models do not start with 'M' #823

Closed caixu0518 closed 1 month ago

caixu0518 commented 1 month ago

Dear BRAKER Team,

I am writing to inquire about an issue I have encountered with gene models generated by BRAKER. In the results from Augustus, I have noticed that many gene models do not start with 'M'. Similarly, when using TransDecoder for prediction, I also observe numerous gene models that do not start with 'M', including some full-length transcripts.

Could you please clarify what might be causing this phenomenon? My concern is that if I were to consider these non-'M' starting gene models as reliable, they could potentially occupy regions that might otherwise be supported by evidence for genuine gene models. This could lead to the removal of gene models supported by stronger evidence.

I would greatly appreciate any insights or guidance you can provide to help resolve my confusion regarding this issue.

Best， Xu

KatharinaHoff commented 1 month ago

This is a duplicate issue with https://github.com/Gaius-Augustus/Augustus/issues/409 . I am closing here.