LeafCutter vs. MAJIQ and comparing software in the fast-moving field of genomics

Abstract

In a recent publication, Li et al. introduced LeafCutter, a new method for detecting and quantifying differential splicing of RNA from RNASeq data. In this work, Li et al. first compared LeafCutter to existing methods, then used it for a study of splicing variations and sQTL analysis from a large set of GTEx samples. While the study was elaborate and comprehensive, we want to highlight several issues with the comparative analysis performed by Li et al. We argue these issues created an inaccurate and misleading representation of other tools, namely MAJIQ and rMATS. More broadly, we believe the points we raise regarding the comparative analysis by Li et al. are representative of general issues we all, as authors, editors, and reviewers, are faced with and must address in the current times of fast paced genomics and computational research.