PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

Correctly estimating isoform-specific gene expression is important for understanding complicated biological mechanisms and for mapping disease susceptibility genes. However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not appropriately corrected, can affect isoform expression estimation and downstream analysis. In this article, researchers from the University of Pennsylvania present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. Thier rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. They evaluate the performance of PennSeq using both simulated data with known ground truth, and using two real Illumina RNA-Seq data sets including one with quantitative real time polymerase chain reaction measurements. Their results indicate superior performance of PennSeq over existing methods, particularly for isoforms demonstrating severe non-uniformity.

rna-seq

Availability – PennSeq is freely available for download at http://sourceforge.net/projects/pennseq.

Hu Y, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M. (2013) PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Research [Epub ahead of print]. [article]
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