Uncertainty in RNA-seq gene expression data

Abstract

RNA-sequencing data is widely used to identify disease biomarkers and therapeutic targets. Here, using data from five RNA-seq processing pipelines applied to 6,690 human tumor and normal tissues, we show that for >12% of protein-coding genes, in at least 1% of samples, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold using the same samples and the same set of RNA-seq reads, raising clinical concern.