Paired-end (PE) sequencing is typically not recommended for QuantSeq FWD (Cat. No. 015, 113 – 115, 129 - 131) and QuantSeq with UDI V2 (Cat. No. 191 - 196), as the quality of Read 2 is very low due to the poly(T) stretch at the beginning of Read 2.
HoweverNevertheless, if QuantSeq FWD lane mixes are libraries can be sequenced in PE mode (i.e., 150bp) but in this case, we recommend discarding Read 2 data and proceeding with Read 1 data only for downstream data analysis (i.e., use only Read 1 for trimming, alignment, read counting, and downstream analyses).
For PE sequencing, QuantSeq REV (Cat. No. 016225) may be used. Please note QuantSeq REV requires a Custom Sequencing Primer (CSP) for Read 1, in order to generate reads that begin at the exact 3' end of the transcript.