Many gene models do not start with 'M'

[caixu0518]

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]

This is a duplicate issue with Gaius-Augustus/Augustus#409 . I am closing here.