Recent progress inNGS technology has enabled high throughput analysis of transcription in various types of cells. The obtained sequences are partial segments of the full-length transcripts. Those reads aremapped to a reference genome by using tools such as Tophat [1], LAST [2], and STAR [3]. The transcribedunitsofRNAs aredetermined fromthemapped reads
by using tools such as Cufflinks [4] and Scripture [5].