Organisms express their phenotypes by competitive gene expression. During decades, researchers have quantitated gene expression levels using DNA microarray method for understanding of molecular biology. However, as sequencing costs decreased, the number of transcriptome analysis using RNA-seq has been increased recently. This new RNA-seq data has not only possibility of confirmation for transcript expression but also confirmation of novel isoform which can extract more diverse analysis results than DNA microarray method. In this research, we introduce experimental and computer scientific perspectives which needed for RNA-seq data analysis and Tuxedo protocol among the various pipeline to detect differentially expressed genes(DEG) and practice of visualization analysis.