rRna gene finder (software) for bacterial whole genome sequence

Question

[hafiz.talhamalik]

I need to find rRna from my whole genome sequenced data of bacterial samples. I have tried RNAmmer & quast plugin for rRNA finding but both tools are not giving any rRNA. RNAmmer gives me an empty file.

Answer 1

[Carambakaracho]

You're question is less clear than you might think:

Do you look for annotation of rRNA in your assembled genome? -> good old tRNAscan-SE or right away full annotation with prokka

Do you want to perform computational rRNA depletion? -> SortMeRNA

[hafiz.talhamalik]

Yeah I am looking for annotation for my assembled genome. I used Prokka and as prokka uses rnammer so like RNAmmer, it didn't gave me any rRNA. Isn't the tRNAscan-SE prog is for tRNA search ???

[Carambakaracho]

oh apologies, my bad, your right tRNAscan-SE provides of course tRNA search. I had good results with barrnap - it's also part of prokka. Though no results with RNAmmer might indicate problems, maybe verify with blasting some 16S gene?

[hafiz.talhamalik]

ok. I will try to that. if u get to know any other tool do let me know