I used SortMeRNA to remove rRNA sequences in my raw RNA-seq data. I got ~95% clean data for 7 out of 8 samples. For the remaining one, I only got ~75%..., around 20% was mapped to the eukaryotic 18s and 28s sequence. Later in the differential expression analysis, the wired sample appeared to be an outgroup in the PCA plot and it cannot be clustered with other replicated samples.
Therefore, I may have to discard this sample in my DE analysis. But I may also skip the rRNA removal step so that it will not cause the problem...What should I do?