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  • RNA-Seq: distinguish lncRNA of smRNA precursors

    Hi everybody,

    I have some data from RNA-seq. This data does NOT come from a library of small RNAs, but comes from a library of mRNAs and total RNA. From this data, I perform an alignment with TopHat, followed by cufflinks and annotation of the genes. After this point, I have a pipeline that extracts the lncRNAs from the other RNAs.

    Once I have the lncRNAs, how could I differentiate the precursors of small RNAs from the "real" lncRNAs? I know that the vast majority of publications performs a BLAST against the existing database of miRNAs, and I have that in mind. However, I would like to ask if there exists another method, software, etc. that takes into account the secondary structure of the lncRNAs in order to say: OK, this might be a precursor of any small RNA (miRNA, siRNA, shRNA,...).

    Do you have some suggestions?

    Thanks in advance.

    PD: I am working with plant transcriptome.
    Last edited by int11ap1; 03-20-2014, 03:55 AM.

  • #2
    UEA has a strategy to find novel miRNA from sequencing data.

    Another interesting method is iMir, however I have not tested yet.

    Comment


    • #3
      Thank you for the reply, TiborNagy. Nevertheless, the packages you suggest work only with small RNA-seq data! What if my library is a cDNA library?

      The aim is to find pre-miRNAs from my annotated lncRNAs.

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