We are currently embarking on an RNAseq project using a sequencing service provider but have a few questions concerning the ribosomal RNA depletion step (Ribo Zero) that would markedly add to the cost of the project.
Our initial quotation without depletion (TruSeq RNA kit) is quite competitive. Is it necessary to carry out the depletion step if the RNA is to be further fractionated via a polyA step? Does anyone have an idea how much ribosomal RNA would carry over past the polyA isolation? Could this ribosomal RNA be depleted via bioinformatics? We realize that its presence would reduce the proportion of sequences of interest but are unsure as to how much it would do so relative to the added cost.
We would appreciate anyone’s thoughts on this and thank-you in advance.