S-IRFindeR: stable and accurate measurement of intron retention
Broseus, L.; ritchie, w. J.
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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/.
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