Gaius-Augustus / TSEBRA

TSEBRA: Transcript Selector for BRAKER
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Combine BRAKER3 and Galba annotation for new, non-model genome #51

Open YanisChrys opened 5 months ago

YanisChrys commented 5 months ago

Hello,

In order to better annotate my reptile genome I have used BRAKER3-ETP and Galba (with ~6 of the closest relative proteomes) and now I am trying to combine them using TSEBRA. The inputs look like this:

BRAKER3 | C:67.6%[S:56.0%,D:11.6%],F:3.6%,M:28.8%,n:7480

GALBA | C:93.3%[S:75.1%,D:18.2%],F:1.6%,M:5.1%,n:7480

This is the command I am using:

singularity exec --bind $WORKDIR /path/to/containers/braker3.sif /opt/TSEBRA/bin/tsebra.py \ --gtf ${galba_gtf},${braker_gtf} \ --hintfiles ${hints_gff2},${hints_gff1} \ --filter_single_exon_genes \ --ignore_tx_phase \ --cfg ${braker_cfg} \ --out ${out_gtf} \ --verbose 1 2> ${log}

I have experimented a lot but I can't find a way to run it that maximises busco and keeps mostly single genes. I have tried the following: