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  • smallRNA annotation

    Hi,

    I'm lookinf for a way to annotate smallRNA from high-throughput sequencing. I've already annotate the reads with miRBase. Now I'm looking to annotate the rest of the reads ( piRNA, snoRNA,...) .

    Is it a R package to do that ? or an another way ?

    Thanks

    N.

  • #2
    nobody knows?

    Comment


    • #3
      Originally posted by NicoBxl View Post
      nobody knows?
      Have you looked in the wiki?
      MirTools is listed there for instance, but i bet there are many more -hopefully the one you are looking for too.
      Last edited by steven; 02-28-2011, 06:26 AM. Reason: small extension

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      • #4
        Thanks,

        Finally here's the pipeline I used

        1. annotation of the reads with miRBase 16 (blast against the reads)
        2. With the rest of the reads, annotation with Rfam 10

        Comment


        • #5
          How exactly do you go about to annotate to Rfam?

          Could you please give me a detailed pipeline?

          Comment


          • #6
            bowtie "Out of memory...."

            I am trying to run bowtie on paired end reads and I am getting the following error:

            Out of memory allocating the ebwt[] array for the Bowtie index. Please try
            again on a computer with more memory.


            Whats wrong here and what can I do without changing computer?

            Comment


            • #7
              how much memory do you have on your computer ? and what is the size of your genome ( is it homo sapiens ? )

              Comment


              • #8
                I moved the thread....

                Comment


                • #9
                  How to annotate ncRNAs in bacteria (for deep sequencing data).
                  suggestions plz
                  Krishna

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