ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

• Published in: PLoS computational biology Vol. 14; no. 8; p. e1006360
• Main Authors: Garrido-Martín, Diego, Palumbo, Emilio, Guigó, Roderic, Breschi, Alessandra
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.08.2018; Public Library of Science (PLoS)
• Subjects: Algorithms; Annotations; Bioinformatics; Biology and life sciences; Computer and Information Sciences; Consortia; Data analysis; Experiments; Genomes; Genomics; Methods; Research and analysis methods; Ribonucleic acid; RNA; RNA sequencing; Scaling; Software; Splicing; Technology application; Visualization; Spain
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1006360

We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software. Compared to the existing versions of programs generating sashimi plots, it uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. ggsashimi is freely available at https://github.com/guigolab/ggsashimi. It is implemented in python, and internally generates R code for plotting.