ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data

Summary Exitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for detection and annotation of exitrons in long-read RNA-seq data. Here we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. A companion tool, AnnotateExitron, reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status, and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data. Availability and Implementation ScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index. Contact [email protected] Supplementary Information Supplementary data are available at Bioinformatics online.