SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data

摘要: Alternative splicing plays a key role in the regulation of central dogma. Four major types alternative have been classified as intron retention, exon skipping, 5 splice sites or donor sites, and 3 acceptor sites. A few algorithms developed to detect junctions from RNA-Seq reads. However, there are tools targeting at exon/intron level. This type analysis may reveal subtle, yet important events splicing, thus help gain deeper understanding mechanism splicing. paper describes user-friendly R package, extracting, annotating analyzing for sequence alignment files RNA-Seq. SplicingTypesAnno can: (1) provide annotation By comparing GTF/GFF file, it identifies novel sites; (2) offer convenient two-level analysis: genome-scale users with high performance computing environment, gene-scale personal computers; (3) generate web report additional BED IGV visualization. is package level It publically available https://sourceforge.net/projects/splicingtypes/files/ http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html.