I see internal priming in my QuantSeq data. How can I prevent this?

Internal priming corresponds to the priming of the oligo(dT) primers to regions other than the polyA tail of mRNAs.

Presence of internal priming in your final data may be the result of:

• Mis-hybridization (please see this FAQ for detailed information and how to prevent mis-priming).

• Incomplete reference annotation: Some transcripts may have different and not yet annotated 3' ends, which might be mistaken for internal priming events.

NOTE: Artificial spike-in transcripts such as the SIRVs or the ERCC spike-in transcripts only have one defined 3' end which provides the only true measure to determine internal priming.