Do some of you remove reads originating from rRNA in silico before testing for differential expression?
Why or why not? Is it worth it? Or is it depending on the analysis pipeline in your opinion?
My data is based on poly-A enrichment of mRNA and about 2-5% of the reads (Illumina SE 100bp) are from rRNA operons.
I plan to use HISAT2>stringtie>ballgown workflow as a first strategy to test for DE. I might later try different methods, depending on the ballgown results.