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

ABSTRACT: 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, we present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution. Instead of making parametric assumptions, we give adequate weight to the underlying data by the use of a non-parametric approach. Our rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, loc

SUBMITTER: Hu Y 

PROVIDER: S-EPMC3919567 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature