Adjust the weighting of RNA-seq evidence and re-run by TSEBRA

[hungweichen0327]

Dear developers,

I used braker3 to predict genes in a tree genome (genome size ~900Mb).

The input data:

1. RNA-seq: RNA extracted from the leaves of the targeted species.
2. Protein database: orthoDB11- Viridiplantae

Based on the result, the number of genes in the braker.gtf from braker3 is quite low (30313) than augustus.hints.gtf (54829).
The gene number in the closed-related species is about 40000 genes. I guess it's due to the small set of RNA-seq data which did not contained samples from the roots, flowers, and seeds.

Thus, how can I re-run the TSEBRA with the lower weighting of RNA-seq evidence?

The script I used is below:
tsebra.py -g ./augustus.hints.gtf -e hintsfile.gff,genemark.gtf -c braker3_adjust.cfg -o ./tsebra_output.gtf

The value of E in the braker3_adjust.cfg is changed from 20 (default) to 1

Is this correct?

Thank you for the help.