Paired-end (PE) sequencing is typically not recommended for QuantSeq FWD (Cat. No. 015, 113 – 115, 129 - 131), as the quality of Read 2 is very low due to the poly(T) stretch at the beginning of Read 2.
However, if QuantSeq FWD lane mixes are sequenced in PE mode, 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. 016) 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.