Combining runs of BRAKER3 with short and long-read RNA-seq

[danielwood1992]

Hello,

I am trying to combine two runs of BRAKER3: one using short reads and protein data, the other using long-reads and protein data (using the braker_lr branch). Would the best way to combine these be to use tsebra.py -g $short_read/braker.gtf -l $long_read/braker.gtf -e $short_read.hintsfile.gff,$long_read/hintsfile.gff -c ~/TSEBRA/config/long_reads.cfg -o $some_dir/tsebra.gtf? Or would it be better to specify the Augustus and GeneMark files separately, and not use the braker.gtf files? (or does it not make a difference?)

Thanks a lot and best wishes,

Daniel Wood