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  • miRNA Discovery

    Dear All,
    I am trying to make pipeline for denovo miRNA discovery so can anyone help with what can be probable methods for discovery of novel miRNA.

  • #2
    try miRdeep, it worked for me.

    Comment


    • #3
      Thank you,
      but can you tel me something in detail about miRdeep, i am fresher to this.
      hoping for quick reply.

      Comment


      • #4


        download the demo file, it's easy to use.

        Comment


        • #5
          Don't forget the seqanswers wiki.
          For instance, looking for "mirna" gives you this.
          Last edited by steven; 03-28-2011, 02:00 AM. Reason: typo

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          • #6
            I am trying out miRDeep, but what should i do in the case where reference genome is not available for mapping!!

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            • #7
              mmh you can try with a related species genome.

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              • #8
                Thank U
                Yes, me trying it with related species. What are the necessary filterations required before using miRDeep. Please do reply!!!!

                Comment


                • #9
                  Is this suitable for Solid reads.

                  Comment


                  • #10
                    I am done with the miRDeep , But how to interpret the prediction file, Especially identifying the novel miRNA

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                    • #11
                      You've a score for each prediction. Higher the score is, better it is.

                      Comment


                      • #12
                        Is miRDeep compatible with Solid reads? How to identify novel miRNA from predicted files.

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                        • #13
                          Have you read the mirDeep publication?

                          miRDeep
                          Deciphering the porcine intestinal microRNA transcriptome. (using miRDeep)
                          Another tool to find miRNAs in sequencing data:
                          MIReNA

                          Comment


                          • #14
                            Thank you,
                            Yes i have gone through its publication. I am having the solid reads and i want to discover novel mirna for which i used mirdeep and the python script to discover them. What is the percentage of its accuracy. Can tis results be considered further.

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                            • #15
                              miRDeep it's just a prediction tool. After that, you've to confirmed them experimentally ( custom RT-PCR stemloop per example )

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