I have data from human tissue biopsies with different diseases. My pipeline was fastqc - trimmomatic - fastqc - star - featurecounts - voom/limma. I removed rRNAs during library prep, and from the Ensembl annotation gtf during the featurecounts step.
Now, I am puzzled to get quite a lot of ribosomal proteins as differentially expressed. I understand that these are not rRNAs, but I have never seen so many in one place.
Should I be worried, or could this be normal biology?