Sailfish-cir is a framework to quantify both linear and circular transcripts from RNA-seq data. Usually, expression values of circular transcripts are estimated by the total number of reads that supporting a head-to-tail junction and its corresponding canonical linear junctions. Sailfish-cir provides a pipeline to estimate both linear and circular RNA expression from high-throughput RNA-seq data using an existing model-based method, Sailfish.
Citation: Li M., Xie X., Zhou J., Sheng M., Yin X., Ko E.A., Zhou T., and Gu W., Quantifying circular RNA expression from RNA-seq data using model-based framework. Bioinformatics, 33, 2131-2139, 2017. doi:10.1093/bioinformatics/btx129