ASTK: a software for comprehensive analysis of alternative splicing

Alternative splicing (AS) is pervasive and a key regulatory mechanism leading to diverse protein isoforms with distinct functions. Next-generation sequencing has enabled genome-wide studies of AS. However, AS analysis of massive amount of transcriptomic data generated by RNAseq is challenging due to the limited functions of current software packages, calling for a comprehensive and flexible pipeline. Here, we present ASTK, a software package combing diverse tools to systematically analyze AS events: including clustering AS genes based on spliced exon lengths, sequence feature extraction, functional enrichment analysis for spliced genes and spliced exons respectively, identifying binding motifs of RNA-binding proteins (RBPs) surrounding splice sites, and characterizing splicing-associated histone marks and chromatin states. ASTK was tested using experimental datasets to show its effectiveness and reliability. In our test cases, we grouped differential AS genes/spliced exons into three classes based on the length of spliced exons, which tend to be enriched into discrete functions. Furthermore, we identified several sequence features and epigenetic marks associated with the inclusion level of spliced exons. Therefore, ASTK will facilitate the functional characterization of AS events and improve our understanding of splicing regulation. ### Competing Interest Statement The authors have declared no competing interest.