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. 2017 Apr 11;35(4):319-321.
doi: 10.1038/nbt.3838.

Reproducible RNA-seq analysis using recount2

Leonardo Collado-Torres  1   2   3 , Abhinav Nellore  4   5   6 , Kai Kammers  1   2   7 , Shannon E Ellis  1   2 , Margaret A Taub  1   2 , Kasper D Hansen  1   2   8 , Andrew E Jaffe  1   2   3   9 , Ben Langmead  1   2   10 , Jeffrey T Leek  1   2
Affiliations

Reproducible RNA-seq analysis using recount2

Leonardo Collado-Torres et al. Nat Biotechnol. .
No abstract available

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Conflict of interest statement

COMPETING FINANCIAL INTERESTS

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Meta-analysis and study comparison facilitated by recount2. (a) The distribution of correlations between gene expression estimates for GTEx v6 from the GTEx portal and the counts calculated in recount2 for protein coding genes. The gene expression counts are highly correlated between both quantifications for almost all genes. (b) A comparison of the fold changes for differential expression between colon and whole blood using the quantifications from GTEx and from recount2 for protein coding genes. The majority of genes have a similar fold-change between the two analyses. (c) A concordance versus rank (i.e., ‘concordance at the top’, CAT) plot showing comparisons between a meta-analysis tissue comparison of whole blood and colorectal tissue in data from the sequence read archive and the GTEx project. When comparing the same tissues, there is a strong concordance between differential expression results on public data and GTEx (orange), less concordance when different tissues are compared (blue) and almost none when comparing different analyses (pink).
Figure 2
Figure 2
Multi-feature-level differential expression analysis is facilitated by recount2. (a) Venn diagram showing the number of expressed regions detected that overlap exons, intergenic regions and intronic regions, including expressed regions that overlap multiple annotation types. Differential expression occurs outside of previously annotated protein-coding regions. (b) An example of a region on chromosome 15 showing differential expression between breast cancer subtypes in an annotated intron. The lines show the average coverage in each group across samples. (c) CAT plot of concordance between gene-level analysis and then exon-, junction- and region-level (DER) analyses shows high concordance across the different feature levels.
See this image and copyright information in PMC

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