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

PLoS Comput Biol. 2018 Aug 17;14(8):e1006360. doi: 10.1371/journal.pcbi.1006360. eCollection 2018 Aug.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Animals
  • Computational Biology / methods*
  • Computers
  • Genome
  • Genomics
  • Humans
  • RNA Splicing / physiology
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Software

Grants and funding

DGM is supported by a "La Caixa"-Severo Ochoa pre-doctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.