Number of ORFs - Githubissues

tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

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Closed EugeneKim76 closed 4 years ago

EugeneKim76 commented 4 years ago

Hi, To my knowledge Prokka uses Prodigal to detect ORFs. Is there any way to know the number of ORFs found by prokka? Best,

tseemann commented 4 years ago

Yes, each ORF becomes a gene (CDS) in the output files.

The prokka.txt tells you:

prokka.txt
organism: Escherichia coli strain 
contigs: 11
bases: 385319
CDS: 180
gene: 180

EugeneKim76 commented 4 years ago

Thanks for quick answer. You mean the number of genes in prokka.txt? For example below, number of ORF is 5100?

tmRNA: 1 tRNA: 54 gene: 5100 CDS: 5045

tseemann commented 4 years ago

No, the number of ORF is 5045. Not all genes code for protein. Some are RNA genes.