I am re-analysing some RNA-seq data that I'm told have high levels of rRNA contamination (not sure how high yet). My usual workflow is salmon -> tximport -> DESeq2
I've seen recommendations that any reads matching rRNA need to removed prior to analysis. Is this still the case with the salmon (alignment-free) protocol? if the rRNA are not in my gtf file, then they will not be quantified and appear in the analysis. Obviously I'll get smaller counts than expected, but should be Ok to proceed with the counts for all the other genes?