Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Xiong, B.; Yang, Y.; Fineis, F.; Wang, J.-P.

doi:10.1101/386938

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bioRxiv · 10.1101/386938

Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Xiong, B.·Yang, Y.·Fineis, F.·Wang, J.-P.

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Abstract

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.

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Xiong, B., Yang, Y., Fineis, F., Wang, J.-P.. 2018-08-08. Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis. https://doi.org/10.1101/386938

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