Intron retention rates (IR)
Intron retention is a specific type of AS that is not necessarily captured by JunctionSeq and can have different biological implications for the control of gene expression. An intron can be retained in the final mature mRNA, coding for a new function (Jacob and Smith, 2017; Monteuuis et al., 2019) or a nonfunctional transcript that is degraded by the nonsense-mediated decay (NMD) (Farlow et al., 2010). We investigated whether DE changes due to WGP and TGP involve mechanisms of IR using theIRFinder pipeline (Middleton et al., 2017). A new reference annotation was built by removing all overlapping features present in the same strain sense of individual introns and then unique identifiers were assigned to each flattened exon. Only regions with high mapping scores as estimated through simulated reads across the genome were identified and included in the flattened annotation file. A read count matrix with all reads overlapping splice junctions was generated and IR rates were estimated as: IR rate = junction reads / (junction reads +intronic reads) for each sample using the IRFinder R package (Middleton et al., 2017).