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Typically, for high quality RNA samples, we recommend to aim aiming for 1% of the sequencing reads mapping to the SIRV reference annotation (SIRVome). Please note that the target RNA content will vary between samples. If you do not know the target RNA content of your sample , you can assume a measure of 2 – 3%, which corresponds to the approximate RNA 3% for mRNA-Seq Library Preps and 4% for rRNA-depletion / total RNA-Seq Library Preps. As an example, the approximate mRNA content of reference RNA samples such as the Universal Human Reference RNA (UHRR) is approximately 2-3%.
For input RNA of low complexity or low quality, including from FFPE tissues, the RNA content is often lower or highly variable. SIRV-mapped reads will be at a higher fraction in these samples due to the intact nature of the SIRVs. Here there are two approaches:
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