I have few libraries that are not rRNA depleted and in each of them we have high percentage of reads that are aligned to rRNA genes. I want to normalize data in order to perform multiple comparisons to find differentially expressed genes.
My question is that if I normalize data with methods like "estimateSizeFactorsForMatrix" from DESeq, does this high percentage of rRNA gene distort normalization?
Do I have to remove reads aligned to rRNA?
what is the best approach to tackle this problem?