I'm pretty confused as to which RNA molecules are depleted during rRNA depletion. Part of my confusion comes from my colleagues questioning me. In my analysis, I aligned RNA-seq reads to a reference fasta which contains all coding sequences for the organism that the reads were collected from. The reference contains many coding sequences which are ribosomal protein coding genes. My understanding is that we want these in the reference. Some colleagues disagree and the literature on this subject is non-existent as far as I can tell. So, do we expect these ribosomal protein coding genes to be in the sample after rRNA depletion, meaning that we definitely want them in our alignment reference? Happy to elaborate further if necessary.