...
Use same input amount
Compare samples at same read depth - down sample if necessary
Same Read 1 length
Do not collapse UMIs, even if UMIs are included in QuantSeq-FWD (with SSS UMI Module)
Recommend including technical replicates to assess handling variability (QSF samples processed separately whereas QSP samples processed together)
Recommend including controls (SIRVs) to assess DEG, if interested in this (compare expected vs observed)
What can also cause differences:
Differences in chemistries and protocol