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Lumenogix NGS provides a convenient method for quantifying expression levels for genes and transcripts.  Quantification is done using cufflinks, which produces values normalized by transcript length and htseq-count, which calculates raw hit count expression values.  In general, normalized expression measures are better used for analyzing isoforms within samples and raw hit count values for differential expression between samples.  The user can easily apply variance reduction algorithms as well as transformation and normalizationto the data matrixes and conduct down-stream expression analysis experiments.