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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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How to apply the species models to another species #891

Open Eden-yike opened 4 days ago

Eden-yike commented 4 days ago

Hi, i have two genomes from the same species, and i run braker3 to train the first genome species model, so how to apply the the first genome species model to the other genome? use parameters "--useexisting --species=first_genome "?

KatharinaHoff commented 4 days ago

It is currently not easily possible to do this at all because both GeneMarkS-T and GeneMark for eukaryotic genomes train. You can’t skip it without accuracy loss. Complete run recommended.

Ke Yi @.***> schrieb am Do. 28. Nov. 2024 um 04:45:

Hi, i have two genomes from the same species, and i run braker3 to train the first genome species model, so how to apply the the first genome species model to the other genome? use parameters "--useexisting --species=first_genome "?

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Eden-yike commented 4 days ago

thanks; so, use parameter "--species=first_genome" to annotate the seconda genome? is that ok ?

KatharinaHoff commented 4 days ago

You have to use a new string for species or delete the first round parameters from the augustus config path.

Ke Yi @.***> schrieb am Do. 28. Nov. 2024 um 05:50:

thanks; so, use parameter "--species=first_genome" to annotate the seconda genome? is that ok ?

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