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

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.

SUBMITTER: Fry J 

PROVIDER: S-EPMC9620817 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature