Circular RNAs (circRNAs) are a class of endogenous long noncoding RNA (lncRNA) molecules formed via the back-splicing of linear RNAs. These biologically active molecules lack poly(A) tails and exist in a covalently closed loop structure. The circRNAs are associated with many biological functions, viz., transcriptional regulations, miRNA sponging, and translation of proteins in a 5′-cap-independent manner. Recently, they have been reported to regulate spermatogenic events, suggesting their significance in diagnosing male infertility. Many bioinformatics pipelines have been developed to predict, annotate, and quantify circRNAs. This chapter describes the workflow for predicting and quantifying circRNAs mapped to back-spliced junctions with a comparison to linear spliced junctions from rRNA-depleted RNA-seq datasets of spermatozoa. The suggested pipeline is particularly useful in species such as goats for which genome annotation datasets are unavailable.