RNA-Seq is increasingly the method of choice for researchers studying the transcriptome. It offers numerous advantages over gene expression arrays.

• Broader dynamic range enables more sensitive and accurate measurement of gene expression.
• Not limited by prior knowledge – captures both known and novel features.
• Can be applied to any species, even if reference sequencing is not available.
• A better value, often delivering advantages at a comparable or lower price per sample than many arrays.
• Gene expression profiling across samples.
• Study of alternative splicing events (differential inclusion/exclusion of exons in the processed RNA product after splicing of a precursor RNA segment) associated with diseases.
• Identification of allele-specific expression, disease-associated single nucleotide polymorphisms (SNPs) and gene fusions to understand, e.g. disease causal variants in cancer.
• Study and identification of transcript abundance and expression, transcript assembly and annotation has become very handy due to RNA-Seq tools.