SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Juan L. Trincado, Juan C. Entizne, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott, Eduardo Eyras (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

311 Citations (Scopus)
279 Downloads (Pure)


Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.

Original languageEnglish
Article number40
Pages (from-to)1-11
Number of pages11
JournalGenome Biology
Publication statusPublished - 23 Mar 2018


  • Alternative splicing
  • Biological variability
  • Differential splicing
  • Differentiation
  • RNA-seq
  • Uncertainty

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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