Chi Zhang, Baohong Zhang, Michael S Vincent and Shanrong Zhao
In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. âÂ€Â˜Union-exonâÂ€Â™ and transcript based approaches are widely used in gene quantification. The âÂ€Â˜Union-exonâÂ€Â™ based approach is simple, but it does not distinguish between isoforms when multiple alternatively spliced transcripts are expressed from the same gene. Because a gene is expressed in one or more transcript isoforms, the transcript based approach is more biologically meaningful than the âÂ€Â˜union exonâÂ€Â™-based approach. However, estimating the expression of individual isoform is intrinsically challenging because different isoforms of a gene usually have a high proportion of genomic overlap. Recently, a number of tools have been developed for RNA-seq isoform quantification. We review those methods and their main features to serve as guidance for users to choose suitable tools for their specific projects.