S-IRFindeR: stable and accurate measurement of intron retention

Accurate quantification of intron retention levels is currently the crux for detecting and interpreting the function of retained introns. Using both simulated and real RNA-seq datasets, we show that current methods suffer from several biases and artefacts, which impair the analysis of intron retention. We designed a new approach to measure intron retention levels called the Stable Intron Retention ratio that we have implemented in a novel algorithm to detect and measure intron retention called S-IRFindeR. We demonstrate that it provides a significant improvement in accuracy, higher consistency between replicates and agreement with IR-levels computed from long-read sequencing data. S-IRFindeR is freely available at: https://github.com/lbroseus/SIRFindeR/.