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DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.

ABSTRACT: RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. We propose a novel pipeline named DegNorm to adjust the read counts for transcript degradation heterogeneity on a gene-by-gene basis while simultaneously controlling for the sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of simulated and real RNA-seq data.

SUBMITTER: Xiong B

PROVIDER: S-EPMC6466807 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.

Xiong Bin B Yang Yiben Y Fineis Frank R FR Wang Ji-Ping JP

Genome biology 20190416 1

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. We propose a novel pipeline named DegNorm to adjust the read counts for transcript degradation heterogeneity on a gene-by-gene basis while simultaneous ...[more]

PMID: 30992037

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