Yes, low quality and FFPE samples can be used with QuantSeq 3' mRNA-Seq FWD and REV kits.
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Some minor protocol modifications for QuantSeq FWD and REV are required and are indicated in the table tables below:
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Preparing FFPE RNA for QuantSeq
The quality of RNA from FFPE tissues can vary greatly. We recommend measuring the DV200 DV200 value (the percentage of RNA greater than 200 nt in length) in addition to RIN values, as RIN values become less meaningful for highly degraded samples.
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When preparing libraries for comparative gene expression profiling, all libraries that will eventually be compared should be amplified using the same number of PCR cycles.
NOTE: The DV200 DV200 value is not a reliable predictor of the required number of PCR cycles needed.
If there are a range of optimal PCR cycle numbers predicted for your samples, you may wish to perform an additional endpoint PCR test to check the library yields are sufficient for sequencing. This is ideally done using half the library volume for a couple of samples that have different cycle number predictions (e.g., lowest, middle, and highest cycle number), and using the average number of cycles for the endpoint PCR (adding one additional cycle to account for using half the library volume). After purifying and quantifying these libraries, you can evaluate the relative yields and adjust the number of PCR cycles accordingly.
NOTE:Additional PCR and purification reagents provided in the PCR Add-on and Reamplification Kit for Illumina V2 (Cat. No. 020.96208) and the Purification Module with Magnetic Beads (Cat. No. 022.96) would be required for this type of endpoint PCR testing.