Assessment of duplication rates in RNA-Seq datasets.
PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed genes. Especially when working with little input material or single cells assessing the fraction of duplicate reads is an important quality control step for NGS data sets. Up to now there are only tools to calculate the global duplication rates that do not take into account the effect of gene expression levels which leaves them of limited use for RNA-Seq data.
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Sayols S, Scherzinger D, Klein H (2016). “dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data.” BMC Bioinformatics, 17, 428. doi: 10.1186/s12859-016-1276-2.