- Open Access
Erratum to: A survey of best practices for RNA-seq data analysis
© The Author(s). 2016
- Received: 17 August 2016
- Accepted: 17 August 2016
- Published: 26 August 2016
The original article was published in Genome Biology 2016 17:13
During editing of the article by Conesa et al. , 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) , eXpress , Sailfish  and kallisto  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  (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 , positional biases in coverage along the transcript (which are accounted for in Cufflinks), average fragment size , and the GC contents of genes (corrected in the EDAseq package ).
The citation for EDAseq should be  (Risso et al. BMC Bioinformatics. 2011;12:480)
The NOISeq R package  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  (Tarazona et al. Nucleic Acids Res. 2015;43:e140)
These effects can be minimized by appropriate experimental design  or, alternatively, removed by batch-correction methods such as COMBAT  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 .
The citation for the RGASP article should be  (Engström et al. Nat Methods. 2013;10:1185–91).
We refer the reader to  for a comprehensive comparison of RNA-seq mappers.
This citation should be  (Engström et al. Nat Methods. 2013;10:1185–91).
Open AccessThis 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.