ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data.
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data.
复制标题
ScanExitronLR：长读长 RNA-seq 数据中退出子剪接事件的表征和定量。
DOI：
10.1093/bioinformatics/btac626
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Yang,Rendong
中科院分区：
文献类型：
--
作者：
Fry,Joshua;Li,Yangyang;Yang,Rendong
SummaryExitron 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 implementationScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index.Supplementary informationSupplementary data are available atBioinformaticsonline.
