after running Trimmomatic and clipping Illumina adapters, I always run a FASTQC to have a look at the quality of my data.
This time I received for 80 % of my samples the info that there are overrepresented sequences. I blasted them, they are no adapters but pre-40s rRNA and mitochondria sequences. Their abundance is around 0.17 %.
My question is, do I have to remove these sequences from my RNA Seq data before calculating differentially expressed genes? If yes, do I have to remove them from all samples, even in those where they are not highlighted as overrepresented?
Thanks for any help!