Both kit versions yield sequences close to the 3' end of transcripts. The difference is in the location of the Read 1 linker sequence. If it is located in the 5' part of the second strand synthesis primer (QuantSeq Forward ( FWD )V2, Cat. No. 015, 113 – 115, 129 - 131191 - 196), NGS reads will be generated towards the poly(A) tail (Figure 1). The FWD version .
QuantSeq FWD is therefore recommended for all gene expression applications. 
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With QuantSeq Reverse (QuantSeq REV V2, Cat. No. 016225), the Read 1 linker sequence is located on the 5' end of the oligodT primer and a oligo(dT) primer. A Custom Sequencing Primer (CSP, included in the kit) is required for sequencing in order to start the read directly at the 3' end (Figure 2). Based on this feature, the exact 3' UTR transcription end site can be pinpointeddetermined.
QuantSeq REV is ideal for applications including alternative polyadenylation site identification and alternative 3' UTR expression studies. 
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