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  • lncRNA differential expression using RNA-seq

    Hi All,
    I have been doing RNAseq for differential expression using standard reference genome mapping and using EdgeR or DESeq to detect differential expression with no problem. I also have extensive microarray and qPCR data for the same samples, so a healthy dose of positive controls for known genes.

    While validating one of my candidate differentially expressed genes (which was a microRNA) y realized that what was actually differentially expressed was novel lncRNA just upstream. After looking through the data, I have found several instances in which I have what appears to be lncRNAs which are greatly induced by my treatment.
    My questions is: is there a way to scan in an unbiased way for yet to be annotated long non-coding genes that are differentially expressed between treatment and control? Would a de-novo assembly strategy like Trinity, followed by edgeR or DEseq work?

    I am working with mouse tissue, BTW

    any suggestions will be greatly appreciated

    Lucia

  • #2
    The problem will always be proving that it is non-coding. Absence of proof is not proof of absence.

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