Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021:2284:181-192.
doi: 10.1007/978-1-0716-1307-8_10.

Computational Analysis of circRNA Expression Data

Giulio Ferrero  1   2 , Nicola Licheri  1 , Michele De Bortoli  2 , Raffaele A Calogero  3 , Marco Beccuti  1 , Francesca Cordero  4
Affiliations

Computational Analysis of circRNA Expression Data

Giulio Ferrero et al. Methods Mol Biol. 2021.

Abstract

Analysis of circular RNA (circRNA) expression from RNA-Seq data can be performed with different algorithms and analysis pipelines, tools allowing the extraction of heterogeneous information on the expression of this novel class of RNAs. Computational pipelines were developed to facilitate the analysis of circRNA expression by leveraging different public tools in easy-to-use pipelines. This chapter describes the complete workflow for a computationally reproducible analysis of circRNA expression starting for a public RNA-Seq experiment. The main steps of circRNA prediction, annotation, classification, sequence reconstruction, quantification, and differential expression are illustrated.

Keywords: Circular RNAs; Noncoding RNAs; RNA sequencing.

PubMed Disclaimer

References

    1. Salzman J (2016) Circular RNA expression: its potential regulation and function. Trends Genet 32:309–316 - DOI
    1. Szabo L, Salzman J (2016) Detecting circular RNAs: bioinformatic and experimental challenges. Nat Rev Genet 17:679–692 - DOI
    1. Hansen TB (2018) Improved circRNA identification by combining prediction algorithms. Front Cell Dev Biol 6:20 - DOI
    1. Gao Y, Wang J, Zheng Y et al (2016) Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun 7:12060 - DOI
    1. Cheng J, Metge F, Dieterich C (2016) Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics 32:1094–1096 - DOI

LinkOut - more resources