Bioinformatics Tools for RNA-seq Gene and Isoform Quantification

In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression.'Union-exon' and transcript based approaches are widely used in gene quantification.The 'Union-exon' 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 'union exon'-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.