RNA sequencing: advances, challenges and opportunities

Recent developments in methods for RNA sequencing have led to an increased understanding of transcriptomes — both qualitative and quantitative. Ongoing developments include advances in direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials. In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.