1. Introduction
VaSP is an R package for discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)
Figure 1. Overview of VaSP. (A). The workflow and functions of VaSP. The input is an R data object ballgown (see ?ballgown) produced by a standard RNA-seq data analysis protocol, including mapping with HISAT, assembling with StringTie, and collecting expression information with R package Ballgown. VaSP calculates the Single Splicing Strength (3S) scores for all splicing junctions in the genome (?spliceGenome) or in a particular gene (?spliceGene), identifies genotype-specific splicing (GSS) events (?BMfinder), and displays differential splicing information (?splicePlot. This function is removed). The 3S scores can be also used for other analyses, such as differential splicing analysis or splicing QTL identification. (B). VaSP estimates 3S scores based on junction-read counts normalized by gene-level read coverage. In this example, VaSP calculates the splicing scores of four introns in a gene X with two transcript isoforms. Only the fourth intron is a full usage intron excised by both the two isoforms and the other three are alternative donor site (AltD) sites or Intron Retention (IntronR), respectively. (C). Visualization of splicing information in gene MSTRG.183 (LOC_Os01g03070), whole gene without splicing scores. (D). Visualization of differential splicing region of the gene MSTRG.183 with splicing score displaying. In C and D, the y-axes are read depths and the arcs (lines between exons) indicate exon-exon junctions (introns). The dotted arcs indicate no junction-reads spanning the intron (3S = 0) and solid arcs indicate 3S > 0. The transcripts labeled beginning with ‘LOC_Os’ indicate annotated transcripts by reference genome annotation and the ones beginning with “MSTRG” are transcripts assembled by StringTie. (Yu et al., 2021)