Monday, December 21, 2009

RNA-Seq gene expression estimation with read mapping uncertainty

Motivation: RNA-Seq is a promising new technology for accurately measuring gene expression levels. Expression estimation with RNASeq requires the mapping of relatively short sequencing reads to a reference genome or transcript set. Because reads are generally shorter than transcripts from which they are derived, a single read may map to multiple genes and isoforms, complicating expression analyses. Previous computational methods either discard reads that map to multiple locations or allocate them to genes heuristically.

Results: We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels. Unlike previous methods, our method is capable of modeling nonuniform read distributions. Simulations with our method indicate that a read length of 20 to 25 bases is optimal for gene-level expression estimation from mouse and maize RNA-Seq data when sequencing throughput is fixed.

Availability: An initial C++ implementation of our method that was used for the results presented in this paper is available at

(source URL, Via Bioinformatics - Advance Access.)