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

Trincado Alonso, Juan Luis, 1987-; Entizne, Juan Carlos; Hysenaj, Gerald; Singh, Babita, 1986-; Skalic, Miha, 1990-; Elliott, David, 1947-; Eyras Jiménez, Eduardo

doi:http://dx.doi.org/10.1186/s13059-018-1417-1

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

Llicència

Citació

Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018 Dec;19(1):40. DOI: 10.1186/s13059-018-1417-1

Resum

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.