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  • (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..?

  • #2
    You can specify the kingdom using -m:
    source

    Comment


    • #3
      Originally posted by TiborNagy View Post
      You can specify the kingdom using -m:
      source
      First, Thanks for your reply.

      -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, 10:23 PM.

      Comment


      • #4
        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

        Comment


        • #5
          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

          Comment

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