Single-read 50 (SR50) sequencing runs are suitable for both QuantSeq versions. Although, for QuantSeq REV For QuantSeq REV sequencing it is favorable to use longer runs (SR100), since starting the read exactly at the 3`UTR will also show the single-read lengths of 75 - 150 bases (SR75 - 150). As the reads start exactly at the 3´UTR, the start of the read includes the A-rich polyadenylation signal, which covers up to 25 nt from the transcription end of the transcript.
As the polyadenylation signal is quite similar for all transcripts, it is better to have longer reads >SR50 available for mapping in order to increase the number of uniquely mapping readswill facilitate higher unique mapping rates.