Hello everyone, I have a fasta files containing genomes of bacterias and I would like to extract only 16s rRNA gene, I have tried with R packages like "micropan" with the function barrnap using the following code
barrnap(genome.file = "file_containing_genome.fasta",bacteria = T,cpu = 8) and the output is the next
Seqid Source Type Start End Score Strand Phase Attributes NC_009925 barrnap:0.7 rRNA 1405563 1405673 4.2e-09 - NA Name=5S_rRNA;product=5S ribosomal RNA NC_009925 barrnap:0.7 rRNA 1409150 1410649 0.0e+00 - NA Name=16S_rRNA;product=16S ribosomal RNA NC_009925 barrnap:0.7 rRNA 5636176 5637675 0.0e+00 + NA Name=16S_rRNA;product=16S ribosomal RNA NC_009925 barrnap:0.7 rRNA 5641152 5641262 4.2e-09 + NA Name=5S_rRNA;product=5S ribosomal RNA
Is there a way to extract the gene with the position provided from this function? or Is there another way to extract this gene?