Yes. Low-quality and FFPE samples can be used with QuantSeq with UDI V2.
Data obtained with QuantSeq with UDI V2 from Fresh-Frozen and FFPE samples, in fact, show a high overlap of detected genes.
Figure | Sequencing data obtained with 10ng input from two different mouse spleen samples, 1M reads, 1cpm, 5cpm and 10cpm (from left to right).
RIN values: 3.7 (FF) and 2.9 (FFPE). DV200 values: 90% (FF) and 9% (FFPE).