Schuierer, Sven and Roma, Guglielmo (2016) The Exon Quantification Pipeline (EQP): a comprehensive approach to the quantification of gene, exon, and junction expression from RNA-seq data. Nucleic Acids Research, 44 (16). e132. ISSN 0305-10481362-4962

Abstract

The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon, and exon-exon junction expression. In contrast to previous counting-based approaches EQP takes only reads into account whose alignment pattern agrees with the splicing pattern of the features of interest. This leads to improved gene expression estimates and the generation of exon counts that allow disambiguating reads between overlapping exons. In addition, EQP also provides a novel way to compute junction counts based on the agreement of the read alignments with the exons on both sides of the junction rather than only quantifying skipped introns, thus providing a uniformly derived set of counts. We evaluated the performance of EQP on both simulated and real Illumina RNA-seq data and compared it with other quantification tools. Our results suggest that EQP provides superior gene expression estimates and we illustrate the advantages of EQP’s exon and junction counts. The provision of uniformly derived high-quality counts makes EQP an ideal quantification tool for differential expression and differential splicing studies. EQP is freely available for download at http://sourceforge.net/projects/XXX

Item Type:	Article
Keywords:	RNA-seq quantification
Date Deposited:	12 Oct 2016 00:45
Last Modified:	12 Oct 2016 00:45
URI:	https://oak.novartis.com/id/eprint/26113