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. 2018 Mar 15;34(6):1066-1068.
doi: 10.1093/bioinformatics/btx690.

DIEGO: detection of differential alternative splicing using Aitchison's geometry

Gero Doose  1   2   3 , Stephan H Bernhart  1   2 , Rabea Wagener  4 , Steve Hoffmann  1   2   5
Affiliations

DIEGO: detection of differential alternative splicing using Aitchison's geometry

Gero Doose et al. Bioinformatics. .

Abstract

Motivation: Alternative splicing is a biological process of fundamental importance in most eukaryotes. It plays a pivotal role in cell differentiation and gene regulation and has been associated with a number of different diseases. The widespread availability of RNA-Sequencing capacities allows an ever closer investigation of differentially expressed isoforms. However, most tools for differential alternative splicing (DAS) analysis do not take split reads, i.e. the most direct evidence for a splice event, into account. Here, we present DIEGO, a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads.

Results: The python tool DIEGO works without isoform annotations and is fast enough to analyze large experiments while being robust and accurate. We provide python and perl parsers for common formats.

Availability and implementation: The software is available at: www.bioinf.uni-leipzig.de/Software/DIEGO.

Contact: steve@bioinf.uni-leipzig.de.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
Performance of DIEGO. (a) Receiver operator statistics for simulated data comparison of DIEGO (close dots) to DEXSeq (solid line), cufflinks (far dots), rMATSturbo (big dashes) and MAJIQ (dots/dashes) on an artificial dataset. (b,c) Time and memory consumption of DIEGO in clustering mode (blue) and DAS mode with different relative group sizes (solid line with dots 1:1, solid line 1:10 group size) compared to DEXSeq (black). (d) Effect of swapping samples between conditions on the number of significant results (Color version of this figure is available at Bioinformatics online.)
See this image and copyright information in PMC

References

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    1. Liu R. et al. (2014) Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. BMC Bioinformatics, 15, 364. - PMC - PubMed

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