Skip to main content

Advertisement

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

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

Erratum

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).

References

  1. 1.

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

Download references

Author information

Correspondence to Ana Conesa or Pedro Madrigal or Ali Mortazavi.

Additional information

The online version of the original article can be found under doi:10.1186/s13059-016-0881-8.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark