Transcriptome analysis is a useful method for identification and understanding of genes. Finding genes that are differentially expressed between conditions is a crucial aspect of transcriptomics. The discovery of RNA seq has revolutionized next-generation sequencing technology. The fact that RNA sequencing does not requires gene probes and provides a precise measure of gene expression over a much wider range proved its credibility over other common techniques. The expressed gene profile and transcriptome data are stored in a database and could be accessed freely. During RNA seq short read mapping to the reference transcriptome (the set of all known transcript RNA sequences for a species) or genome in the database, a variety of database search tools and alignment methods become visible. There are a variety of applications that help align short reads generated by fragment sequencing. The study of expressed genes is aided by quantifying reads that align to the reference genome or transcriptome. RNA sequencing gives crucial information regarding alternative splicing and gene isoforms, in addition to differential gene expression.