Alternative splicing analysis benchmark with DICAST

Abstract

Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for the analysis of alternative splicing integrating 11 splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.

Publication
bioRxiv
Amit Fenn
Amit Fenn
PhD student
Olga Tsoy
Olga Tsoy
Group Leader

I’m a group leader of Computational Genomics and Transcriptomics group. I focus on the BMBF funded Sys_CARE project about alternative splicing in cardiac and renal diseases. I graduated from Lomonosov Moscow State University and did PhD in Kharkevich Institute in Moscow at professor Gelfand lab. There I studied the evolution of transcriptional regulatory networks in bacteria. During my PhD I shortly stayed at Stowers Institute for Medical Research, Kansas-City, where I went on working on regulation of bacterial metabolic pathways. As a research scientist, I worked in Skolkovo Institute of Science and Technology, Moscow on 3D chromatin structure analysis.

Tim Faro
Tim Faro
Student research assistant
Fanny Rößler
Fanny Rößler
Student research assistant
Zakaria Louadi
Zakaria Louadi
PhD student
Chit Tong Lio
Chit Tong Lio
PhD student