Bioinformatics Tools for RNA-seq Gene and Isoform Quantification

Chi Zhang, Baohong Zhang, Michael S Vincent, Shanrong Zhao
2016 Journal of Next Generation Sequencing & Applications  
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
more » ... '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.
doi:10.4172/2469-9853.1000140 fatcat:5ov3cuwjrngfnjicxofzlw6rd4