Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

RNA-Seq enables rapid sequencing of total cellular RNA and should allow the reconstruction of spliced transcripts in a cell population. Trapnell et al. achieve this and transcript quantification using only paired-end RNA-Seq data and an unannotated genome sequence, and apply the approach to characterize isoform switching over a developmental time course. High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and...