Fig. 1

A comprehensive approach for annotation and quantification of circRNAs. A As a first step towards using SRCP, we generated a comprehensive list of all possible circRNAs in a given tissue/species. We generated this list by merging circRNA coordinates provided by different pipelines. B We then reannotate the initial list to obtain one specific set of coordinates for each candidate circRNA. To do so, we rely on the fact that most circRNAs are flanked by already annotated splice sites. Then, if the start coordinates and the end coordinate of the circRNA are both exactly on a 5′ and 3′ boundaries of the transcript’s exons, we compute a score of 2. (ii) If only one coordinate is exactly on an exon boundary, the score is 1. (iii) If neither coordinate is on any exon boundary, the score is 0. We keep the transcript with the highest score. C We determine the cutoff (false-positive and false-negative rate) based on RNaseR sensitivity and expression level. Then we obtain a circRNA index. Importantly, circRNAs from other lists and/or databases can be added to enrich the circRNA index. D Once the circRNA index is set up, SRCP allows accurate quantification of circRNA reads