Question: rRna gene finder (software) for bacterial whole genome sequence
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gravatar for hafiz.talhamalik
16 months ago by
Pakistan
hafiz.talhamalik230 wrote:

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.

ADD COMMENTlink modified 16 months ago by Carambakaracho2.2k • written 16 months ago by hafiz.talhamalik230
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gravatar for Carambakaracho
16 months ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:

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

ADD COMMENTlink written 16 months ago by Carambakaracho2.2k

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 ???

ADD REPLYlink modified 16 months ago • written 16 months ago by hafiz.talhamalik230

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?

ADD REPLYlink modified 16 months ago • written 16 months ago by Carambakaracho2.2k

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

ADD REPLYlink written 16 months ago by hafiz.talhamalik230
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