TY - JOUR
T1 - ScanExitronLR
T2 - characterization and quantification of exitron splicing events in long-read RNA-seq data
AU - Fry, Joshua
AU - Li, Yangyang
AU - Yang, Rendong
N1 - Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected].
PY - 2022/11/1
Y1 - 2022/11/1
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btac626
DO - 10.1093/bioinformatics/btac626
M3 - Article
C2 - 36099042
AN - SCOPUS:85141004194
SN - 1367-4803
VL - 38
SP - 4966
EP - 4968
JO - Bioinformatics
JF - Bioinformatics
IS - 21
ER -