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. 2022 Oct 31;38(21):4966-4968.
doi: 10.1093/bioinformatics/btac626.

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

Joshua Fry  1   2 , Yangyang Li  1 , Rendong Yang  1
Affiliations

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

Joshua Fry et al. Bioinformatics. .

Abstract

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 the 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 individual transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. In addition, ScanExitronLR optionally 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.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
(A) Description of ScanExitronLR and companion tool AnnotateExitron. (B) Schematic representation of the difference between truncation, truncation plus substitution and frameshift inducing exitron splicing events. (C) Simulation results from ONT long-reads at 80%, 85%, 90%, 95% and 100% mean read accuracy levels. Dotted lines indicate simulation results from ScanExitron on 75 bp read length Illumina short-reads. (D) Mean accuracy for each detected exitron, defined as (algorithm-reported AO)/(ground-truth AO). Error bars represent 95% confidence intervals
See this image and copyright information in PMC

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