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Old 04-09-2014, 07:47 PM   #1
Hyunmin
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Location: Seoul, Korea

Join Date: Feb 2012
Posts: 13
Default (Problem) Prediction rRNA with rnammer 1.2

Hi,

I tried to predict the rRNA in scaffold. (de novo assembly genome)
My sample is human genome and I set the euk with rnammer param.

My command..
perl rnammer -S euk -multi -gff rnammer.gff -f rnammer.fasta -h rnammer.report in.scaffold.fa

But, I got the only result (8s_rRNA)

Why I can the result like 5S, 18S, 28S rRNA..?
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Old 04-11-2014, 05:21 AM   #2
TiborNagy
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Default

You can specify the kingdom using -m:
source
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Old 04-14-2014, 11:19 PM   #3
Hyunmin
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Location: Seoul, Korea

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Default

Quote:
Originally Posted by TiborNagy View Post
You can specify the kingdom using -m:
source
First, Thanks for your reply.

Quote:
-m Molecule type can be 'tsu' for 5/8s rRNA, 'ssu' for 16/18s rRNA,
'lsu' for 23/28s rRNA or any combination seperated by comma.
Yes, I know it.

but I tried to already it . and you know "-multi" is the same "-m tsu, ssu, lsu".

I have no idea. and I solved it with another method. (just BLAST to reference rRNA fasta)

Last edited by Hyunmin; 04-14-2014 at 11:23 PM.
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Old 08-01-2014, 08:50 AM   #4
sreyesch
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Default

Quote:
Originally Posted by Hyunmin View Post
First, Thanks for your reply.

Yes, I know it.

but I tried to already it . and you know "-multi" is the same "-m tsu, ssu, lsu".

I have no idea. and I solved it with another method. (just BLAST to reference rRNA fasta)
Don't know if this thread is still open, but to clarify, -multi and -m option are different int RNAmmer

-multi it's use to run the system in parallel, multiple sequences and strand at the same time

-m indicates which predictions you want to do, if you want all it should be 'tsu,ssu,lsu'

Hope that it helps
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Old 06-17-2017, 07:04 AM   #5
Jassipox
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Location: india

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Default RNAmmer output related error

Dear Member,

I have configured RNAmmer in Ubuntu as per manual :

my $INSTALL_PATH = "/home/srb/RNAmmer_2";

$HMMSEARCH_BINARY = "/home/srb/RNAmmer_2/hmmer-2.3.2/hmmsearch"

[Used, hmmer: version 2.2]

command:


perl ./RNAmmer_2/rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport -f output.fa ecoli.fsa


but I have not get any output from this and instead of that temporary file 18807.tsu.cf and temp.18807.fsa has generated.


Any body can suggest me where I am doing wrong or How can I annotate my data.

Looking forward for any related suggestion for this.


Thank you
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