CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets

Covalently closed circular RNAs (circRNAs) produced by back-splicing of exon(s) are co-expressed with their cognate linear RNAs from the same gene loci. Most circRNAs are fully overlapped with their cognate linear RNAs in sequences except the back-spliced junction (BSJ) site, thus challenging the computational detection, experimental validation and hence functional evaluation of circRNAs. Nevertheless, specific bioinformatic pipelines were developed to identify fragments mapped to circRNA-featured BSJ sites, and circRNAs were pervasively identified from non-polyadenylated RNA-seq datasets in different cell lines/tissues and across species. Precise identification and quantification of circRNAs provide a basis to further understand their functions. Here, we describe detailed computational steps to annotate and quantify circRNAs using a series of CIRCexplorer pipelines.

Automated summary

Covalently closed circular RNAs (circRNAs) are produced through back-splicing of exons and are co-expressed with linear RNAs from the same gene loci. While most circRNAs overlap fully with their linear counterparts in sequences, specific bioinformatic pipelines have been developed to identify fragments mapped to circRNA-featured back-spliced junction (BSJ) sites. This has led to widespread identification of circRNAs from non-polyadenylated RNA-seq datasets in various cell lines/tissues and across species.