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dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

Sergi Sayols, Denise Scherzinger, View ORCID ProfileHolger Klein
doi: https://doi.org/10.1101/046243
Sergi Sayols
1Bioinformatics Core Facility, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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  • For correspondence: S.SayolsPuig@imb-mainz.de holger.klein@gmail.com
Denise Scherzinger
1Bioinformatics Core Facility, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
2FH Bingen, Germany.
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Holger Klein
1Bioinformatics Core Facility, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
3Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany
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  • ORCID record for Holger Klein
  • For correspondence: S.SayolsPuig@imb-mainz.de holger.klein@gmail.com
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Abstract

Background 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.

Results Here we present the tool dupRadar, which provides an easy means to distinguish artefactual from natural duplicate reads in RNA-Seq data. dupRadar assesses the fraction of duplicate reads per gene dependent on the expression level. Apart from the Bioconductor package dupRadar we provide shell scripts for easy integration into processing pipelines.

Conclusions The Bioconductor package dupRadar offers straight-forward methods to assess RNA-Seq datasets for quality issues with PCR duplicates. It is aimed towards simple integration into standard analysis pipelines as a default QC metric that is especially useful for low-input and single cell RNA-Seq data sets.

  • List of abbreviations

    RPK
    reads per kilobase
    PCR
    polymerase chain reaction
    UMI
    unique molecular identifiers
    QC
    quality control
    ChIP
    chromatin immunoprecipitation
    bp
    base pair
    NGS
    next-generation sequencing
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted March 29, 2016.
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    dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
    Sergi Sayols, Denise Scherzinger, Holger Klein
    bioRxiv 046243; doi: https://doi.org/10.1101/046243
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    dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
    Sergi Sayols, Denise Scherzinger, Holger Klein
    bioRxiv 046243; doi: https://doi.org/10.1101/046243

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