Analyzing Prokaryotic RNA-Seq Data: A Case Study Identifying Holo-Fur Regulated Genes in Campylobacter jejuni.

In recent years, RNA-seq has become an important method in the process of measuring gene expression in various cells and organisms. This chapter will detail all the bioinformatic steps that should be undertaken to determine differentially expressed genes from a typical RNA-seq experiment. Each step will be clearly explained in "non-bioinformatic" terminology so that readers embarking on RNA-seq analysis will be able to understand the rationale and reasoning behind each step. Moreover, the exact command lines used to process the data will be presented along with a description of the various flags and commands.