In the version of this article initially published, the computer script in Box 1 sections B and C, and in Procedure Step 1, contained errors: the last section of the final three lines of the script had 'C1' where it should have been 'C2', as follows:
C1_R1_2.fq should have been C2_R1_2.fq
C1_R2_2.fq should have been C2_R2_2.fq
C1_R3_2.fq should have been C2_R3_2.fq
Users are also directed to an official release version of Cufflinks (version 1.3.0) that produces nearly identical results to those shown in the manuscript, which were produced by Cufflinks 1.2.1 (an unofficial and undocumented development build that was the latest build available when the manuscript was originally written). The script in Procedure Step 16 and the data in Table 5 have been updated to reflect the output of version 1.3.0. The errors have been corrected in the HTML and PDF versions of the article.
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The online version of the original article can be found at 10.1038/nprot.2012.016
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Trapnell, C., Roberts, A., Goff, L. et al. Correction: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 9, 2513 (2014). https://doi.org/10.1038/nprot1014-2513a
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DOI: https://doi.org/10.1038/nprot1014-2513a
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