I want to study ribosomal RNA expression and potential processing sites in bacteria. To such effect, I want to perform an RNA-Seq experiment in order to analyze potential rRNA transcripts isoforms and processing sites.
Conventional RNA-Seq experiments are not designed for the analysis of rRNA expression and generally include a RNA depletion step, which reduces rRNA signal. Notice rRNA in bacteria accounts for ~90% of total RNA.
In the context of studying rRNA processing, would the RNA-Seq approach be appropriate? If so, what rRNA treatment would you recommend to study rRNA expression levels and processing?"
Thank you in advance.