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  • denovo assembly for small rna sequencing

    Hi,
    I am working on small RNA reads for micro RNA analysis. I am using velvet for denovo assembly. Can some one suggest a good tool for denovo assembly for small rna reads.

    Regards
    Vishwesh

  • #2
    Why do you want to assemble small RNSs? Size of small RNSs are smaller than the read size.

    Comment


    • #3
      I want to make a assembly to for finding existing micro RNA and novels ones also... Since there is no reference genome for the species I deal with I thought I could try to build the hairpin structure of the micro RNA using denovo assembly..

      Regards
      Vishwesh

      Comment


      • #4
        I guess you would not find whole hairpins (except if you use a very special library preparation). Even detection of miRNA* is also hard. If you would like to find known miRNAs, align reads agains mirBase.

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        • #5
          Thanks. Our aim is to find novel micro RNA. Can this be done with denovo assembly?

          Vishwesh

          Comment


          • #6
            What I would do is assemble to the miRNA database and examine the reads which don't align. Most will be tRNA though.

            Comment

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