Expression is quantified by counting the number of reads that mapped to each locus in the transcriptome assembly step. Expression can be quantified for exons or genes using contigs or reference transcript annotations.[1] These observed RNA-Seq read counts have been robustly validated against older technologies, including expression microarrays and qPCR.[46][69] Examples of tools that quantify counts are HTSeq,[70] FeatureCounts,[71] Rcount,[72] maxcounts,[73] FIXSEQ,[74] and Cuffquant.