Studies and quantifies high-throughput RNA-Seq datasets. R-SAP employs a hierarchical decision-making procedure to characterize various classes of transcripts. It compares reference genome mappings of RNA-Seq reads with the genomic coordinates of known and well-annotated transcripts. It is able to recognize known and new RNA isoforms and, chimeric transcripts. This tool can discover alternative splicing (AS) and chimeric transcripts.