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  • Erratum
  • Open Access

Erratum to: A survey of best practices for RNA-seq data analysis

Genome Biology201617:181

  • Received: 17 August 2016
  • Accepted: 17 August 2016
  • Published:

The original article was published in Genome Biology 2016 17:13


During editing of the article by Conesa et al. [1], an error was introduced to some of the citations, such that incorrect references were provided for some articles the second time they were cited. The following sentences are affected:

Algorithms that quantify expression from transcriptome mappings include RSEM (RNA-Seq by Expectation Maximization) [40], eXpress [41], Sailfish [35] and kallisto [42] among others. These methods allocate multi-mapping reads among transcript and output within-sample normalized values corrected for sequencing biases [35, 41, 43].

The citation for Sailfish should be [34] (Patro et al., Nat Biotechnol. 2014;32:463–4) in both sentences.

Additional factors that interfere with intra-sample comparisons include changes in transcript length across samples or conditions [50], positional biases in coverage along the transcript (which are accounted for in Cufflinks), average fragment size [43], and the GC contents of genes (corrected in the EDAseq package [21]).

The citation for EDAseq should be [20] (Risso et al. BMC Bioinformatics. 2011;12:480)

The NOISeq R package [20] contains a wide variety of diagnostic plots to identify sources of biases in RNA-seq data and to apply appropriate normalization procedures in each case.

The citation for NOISeq should be [19] (Tarazona et al. Nucleic Acids Res. 2015;43:e140)

These effects can be minimized by appropriate experimental design [51] or, alternatively, removed by batch-correction methods such as COMBAT [52] or ARSyN [20, 53].

The citations for ARSyN should be [19, 53] (Tarazona et al. Nucleic Acids Res. 2015;43:e140, Nueda et al. Biostatistics. 2012;13:553–66).

All these approaches are generally hampered by the intrinsic limitations of short-read sequencing for accurate identification at the isoform level, as discussed in the RNA-seq Genome Annotation Assessment Project paper [30].

The citation for the RGASP article should be [29] (Engström et al. Nat Methods. 2013;10:1185–91).

We refer the reader to [30] for a comprehensive comparison of RNA-seq mappers.

This citation should be [29] (Engström et al. Nat Methods. 2013;10:1185–91).



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Authors’ Affiliations

Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA
Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012 Valencia, Spain
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, CB2 0SZ, UK
Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, 46020, Valencia, Spain
Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 77 Stockholm, Sweden
Center for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176 Stockholm, Sweden
Science for Life Laboratory, 17121 Solna, Sweden
Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, 00014 Helsinki, Finland
School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6BC, Canada
Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
Key Lab of Bioinformatics/Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, 100084, China
School of Life Sciences, Tsinghua University, Beijing, 100084, China
Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA


  1. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. Genome Biol. 2016;17:13.View ArticlePubMedPubMed CentralGoogle Scholar


© The Author(s). 2016