I am looking at E. coli RNAseq data (generated from the Kapa RNA Hyper prep kit). Someone recommended I specifically remove rRNA from the data before mapping against the genome to calculate differentially expressed genes.
I did some more reading online, and I found a few papers that don't specifically mention this step for microbial RNAseq experiments (i.e. Yung et al 2016, Tan et al 2015), and other posts that suggest specific rRNA removal is not needed (i.e. this, but for mouse, not microbes).
I'd love to hear if anyone has any definitive resources to share on this subject -- thanks in advance!