Fig 2. The workflow of mapping RNA-Seq reads to a reference genome and calculating gene expression values.

The blue boxes denote the tools (TopHat2, Bowtie2, MULTICOM-MAP, HTSeq, Cufflinks) used in the steps of mapping RNA-Seq reads to a reference genome and calculating gene expression values. The external input information is represented by brown boxes and the output information is represented by green boxes. The information flow between these components is denoted by arrows.