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rRna gene finder (software) for bacterial whole genome sequence
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14 months ago
Pakistan

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.

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14 months ago
Carambakaracho ♦ 1.2k
Switzerland/Basel

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

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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 ???

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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?

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

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