Why is RNA-seq considered superior to microarrays?

RNA-Seq technology does not require species or transcript-specific probes. It is able to detect novel transcripts, single nucleotide variants, gene fusions, indels, and other formerly unknown changes that microarrays are unable to do. Another advantage RNA-Seq has is that it provides higher specificity and sensitivity. RNA-Seq detects a higher percentage of differentially expressed genes, even genes with low expression. RNA-seq is also capable of simple detection of rare and low-abundance transcripts. Sequencing depth can readily be increased to detect rare transcripts, weakly expressed genes, or single transcripts per cell. Microarray hybridization gene expression is limited by background at the low end and signal saturation at the high end. In contrast, RNA-Seq generates discrete, digital sequencing read counts, and is able to quantify expression across a wider dynamic range (>10^5 for RNA vs 10^3 for microarrays).