The 30th International Conference on Arabidopsis Research (ICAR 2019)

638 / 2019-04-28 14:37:37

SEECR: a novel way to quantify splicing

Alternative Splicing,Splicing,bioinformatics,RNA-Seq

Plenary track > RNA Biology

Alternative Splicing (AS) plays a critical role in conferring phenotypic plasticity and has the potential to contribute to environmental acclimation/adaptation in plants. Current efforts to quantify AS in short-read RNA-seq samples either attempt to estimate transcript isoform abundance, or compare occurrences of various mutually exclusive splicing events. In this work we describe the conceptual development of Splicing Efficiency, an explicit quantification of splice site utilisation at the level of individual base pairs; and describe its transcriptome-wide implementation in the bioinformatic tool SEECR (Splicing Efficiency Estimation for Comparison using RNA-seq). We further demonstrate multiple applications SEECR, which have major implications for our understanding of AS.