Hi Everyone, I have been using edgeR for quite sometime. Most of our RNAseq data comes from infectious organisms like Malaria and Tryps. Our libraries generally have 10 to 20% of the reads coming from rRNA genes (not sure if this is the typical value for other organisms/protocols). All these days, I have been ignoring them while doing the DE analysis using edgeR. I am NOT interested in differential expression of rRNA genes, but, worrying that excluding them from edgeR might bias the library size calculations. On the other hand, including them might introduce bunch of outliers (these rRNA genes have very high read counts). I could not intuitively decide one over other. So, asking for a help from experts. Does this change if libraries have varying amount of rRNA contamination. Say, one set of libraries have 20% rRNA and another has 40%. Thanks a bunch in advance, Gowthaman -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct). [[alternative HTML version deleted]]