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Related Concept Videos

RNA Splicing01:32

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.

Diego Garrido-Martín1,2, Emilio Palumbo1,2, Roderic Guigó1,2,3

  • 1Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

Plos Computational Biology
|August 18, 2018
PubMed
Summary
This summary is machine-generated.

ggsashimi is a new tool for visualizing RNA sequencing splicing events. It generates sashimi plots for single or multiple samples, aiding in the analysis of gene expression across experiments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Splicing events are crucial for gene expression regulation.
  • Visualizing splicing across multiple samples is essential for comprehensive analysis.
  • Existing tools for sashimi plot generation have limitations.

Purpose of the Study:

  • To introduce ggsashimi, a novel command-line tool for visualizing RNA sequencing (RNA-seq) splicing events.
  • To enable the creation of both individual and aggregated sashimi plots across multiple samples.
  • To provide an annotation-independent and scalable solution for splicing event visualization.

Main Methods:

  • ggsashimi is a Python-based command-line tool.
  • It utilizes popular bioinformatics file formats.
  • The tool internally generates R code for plotting, allowing visualization of large genomic regions by scaling segments.

Main Results:

  • ggsashimi generates sashimi plots for individual RNA-seq experiments.
  • It uniquely supports aggregated sashimi plots for groups of experiments.
  • The tool is annotation-independent and handles large genomic regions effectively.

Conclusions:

  • ggsashimi offers a flexible and powerful solution for visualizing RNA-seq splicing events.
  • Its ability to aggregate plots across samples provides novel insights into differential splicing.
  • The tool's design addresses limitations of existing sashimi plot generators.