design: Quantify gene and transcript abundances from single-end or paired-end RNA-Seq data usingRSEM, RSEM computes maximum likelihood abundance estimates using the ExpectationMaximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) andvariable-length reads, fragment length distributions, and quality scores, to determine which transcriptsare isoforms of the same gene. In addition to the default RSEM, customers can also use Kallisto andSalmon. FPKM and TPM method is used to calculated expression level, FPKM represents fragmentsper kilpbase of exon model per million mapped reads, TPM represents transcript per million mappedreads. The FPKM and TPM are able to eliminate the influence of different gene length and sequencingdiscrepancy on the calculation of gene expression. Therefore, the calculated gene expression can bedirectly used for comparing the difference of gene expression among samples