Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2

Abstract Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods...

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Bibliographic Details
Published in:Briefings in bioinformatics 2022-01, Vol.23 (1)
Main Authors: Gaffo, Enrico, Buratin, Alessia, Dal Molin, Anna, Bortoluzzi, Stefania
Format: Article
Language:English
Subjects:
Biological activity
Computer applications
Problem Solving Protocol
Ribonucleic acid
RNA
RNA - genetics
RNA Splicing
RNA, Circular
RNA-Seq
Robustness
Splicing
Transcriptome
Transcriptomes
Whole Exome Sequencing
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Summary:Abstract Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterized by low discovery rates and performance dependent on the analysed data set. We developed CirComPara2 (https://github.com/egaffo/CirComPara2), a new automated computational pipeline for circRNA discovery and quantification, which consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptome characterization.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbab418