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Erratum to: A survey of best practices for RNA-seq data analysis
Genome Biology volume 17, Article number: 181 (2016)
The Original Article was published on 26 January 2016
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
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. Genome Biol. 2016;17:13.
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The online version of the original article can be found under doi:10.1186/s13059-016-0881-8.
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Conesa, A., Madrigal, P., Tarazona, S. et al. Erratum to: A survey of best practices for RNA-seq data analysis. Genome Biol 17, 181 (2016). https://doi.org/10.1186/s13059-016-1047-4
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DOI: https://doi.org/10.1186/s13059-016-1047-4