Barrnap_2020-10-31.sh

# Get 16s sequences from input genomes in fasta format

module load perl/5.28.0
module load hmmer/3.2.1
module load bedtools/2.27.1
module load barrnap/0.9

barrnap MBAD.fna > barrnap_MBAD.gff3
bedtools getfasta -fi MBAD.fna -bed barrnap_MBAD.gff3 -fo rRNA_seq_MBAD.fasta -name -s

barrnap RHO3_bin_12.fna > barrnap_RHO3_bin_12.gff3
bedtools getfasta -fi RHO3_bin_12.fna -bed barrnap_RHO3_bin_12.gff3 -fo rRNA_seq_RHO3_bin_12.fasta -name -s