Gene prediction

Predict genes using Prodigal

Source the configuration file:

source conf_cluster.conf

Create a new folder for gene prediction:

mkdir -p $wd/$PRJ_NAME/3_Gene_Prediction

Run Prodigal:

prodigal -i $ASSEMB_READS/d.$PRJ_NAME.idba/contig.fa \
-d $GENE_PRED/prodigal.idba.$PRJ_NAME.fasta \
-a $GENE_PRED/prodigal.idba.$PRJ_NAME.faa \
-o $GENE_PRED/prodigal.idba.$PRJ_NAME.gbk \
-p meta

Have a look to the created files:

cd $GENE_PRED
ll