Visualization of circular RNAs and their internal splicing events from transcriptomic data

Yi Zheng; Fangqing Zhao

doi:10.1093/bioinformatics/btaa033

Visualization of circular RNAs and their internal splicing events from transcriptomic data

Bioinformatics. 2020 May 1;36(9):2934-2935. doi: 10.1093/bioinformatics/btaa033.

Authors

Yi Zheng¹, Fangqing Zhao^{1

2}

Affiliations

¹ Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
² Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.

PMID: 31950978
DOI: 10.1093/bioinformatics/btaa033

Abstract

Summary: Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples.

Availability and implementation: https://sourceforge.net/projects/ciri/files/CIRI-vis.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

RNA / genetics
RNA Splicing
RNA, Circular*
RNA, Messenger
Sequence Analysis, RNA
Transcriptome*

Substances

RNA, Circular
RNA, Messenger
RNA