RNA-seq (RNA sequencing) uses high-throughput (HTS) data to reveal the presence and quantity of RNA in a biological sample at a given moment in time. In the training available at http://galaxyproject.github.io/RNA-Seq/tutorials/ref_based, we introduce the bioinformatics methods to analyze RNA-seq data using a reference genome. The toy datasets were extracted from the study of Brooks et al. 2011.