RT Journal Article
SR Electronic
T1 Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 386938
DO 10.1101/386938
A1 Bin Xiong
A1 Yiben Yang
A1 Frank R. Fineis
A1 Ji-Ping Wang
YR 2018
UL http://biorxiv.org/content/early/2018/08/07/386938.abstract
AB RNA-seq is a high-throughput assay to profile transcriptional activities in cells. Here we show that transcript degradation is gene-/sample-specific and presents a common and major source that may substantially bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for the degradation bias. We propose a novel pipeline named DegNorm (stands for degradation normalization) to adjust read counts for transcript degradation heterogeneity on a gene-by-gene basis while simultaneously controlling the sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of real RNA-seq data and simulated data.