gene annotation training
Hi, it seems to be possible to train Augustus with help of BUSCO.
- Is it possible to include also Genebank's proteins to increase the number of genes for the annotation?
- Is it possible also to train other annotation tools?
conda activate busco
export BUSCO_CONFIG_FILE=/work/team/assembly/busco-config.ini
run_BUSCO.py -i $1 -o busco-$1 -l $2 -m geno --cpu 1 --long -sp $3 --augustus_parameters='--progress=true'
busco_output="run_busco-$1/augustus_output/retraining_parameters"
specie=\$(basename \${busco_output}/*_parameters.cfg _parameters.cfg)
augustus_species="/work/waterhouse_team/miniconda2/envs/augustus/config/species/"
mkdir \${augustus_species}/\$specie
cp \${busco_output}/* \${augustus_species}/\$specie
conda deactivate
conda activate augustus
augustus --species=\$specie --gff3=on ${1} > $4
Thank you in advance,
Michal