The RSEM software workflow. The standard RSEM workflow (indicated by the solid arrows) consists of running just two programs (rsem-prepare-reference and rsem-calculate-expression), which automate the use of Bowtie for read alignment. Workflows with an alternative alignment program additionally use the steps connected by the dashed arrows. Two additional programs, rsem-bam2wig and rsem-plot-model, allow for visualizing the output of RSEM. RNA-Seq data can also be simulated with RSEM via the workflow indicated by the dotted arrows.