RNA-seq utilizes the sequencing technology to assay the presence and quantity of RNA molecules in the given sample. RNA-seq offers many advantages and supersede the microarray technology that was introduced in 2000s. This includes detects known and novel transcripts, increased specificity and sensitivity, and identification of low-abundance transcripts and isoforms with sufficient sequencing depth. RNA-seq has also been used to discover alternative splicing variants, chimeric RNAs result from fusion genes and RNA editing sites. We can compare RNA-seq data between conditions to detect differences across groups of samples in terms of (1) gene-level expression, (2) transcript/isoform-level expression, and (3) transcript/isoform usage within a gene.