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Long non-coding RNAs (lncRNA) are RNAs longer than 200 nucleotides with low coding potential but with critical regulatory functions. The BMKCloud lncRNA pipeline is designed to analyze rRNA depleted libraries with a high quality, well annotated reference genome, by analysing lncRNA and mRNA expression together. After read trimming and quality control, reads are aligned to the reference genome to assemble transcripts, and subsequent gene structure analysis reveals alternative splicing and novel genes. Transcripts are identified as mRNAs or lncRNAs, and differential expression analysis identifies differentially expressed lncRNAs, their targets and differentially expressed genes (DEGS). Both DEGs and differentially expressed lncRNA targets are functionally annotated to find enriched functional categories.




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