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
SPORTS1.0 is a pipeline to anotate and quantify small RNAs from RNA-seq data, which is optimized for rRNA- and tRNA-derived small RNAs. In addition, SPORTS1.0 can predict potential RNA modification sites using nucleotide mismatch information. SPORTS1.0 is precompiled to annotate small RNAs for a wide range of species across bacteria, fungi, plants, and animals.
Citation: Shi J., Ko E.A., Sanders K.M., Chen Q., and Zhou T., SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Genomics, Proteomics & Bioinformatics, 16, 144-151, 2018. doi:10.1016/j.gpb.2018.04.004