I am trying to analyze the RNA Seq samples that were sequenced using Lexogen QuantSeq 3"UTR platform with NextSeq sequences. I was wondering if we could use the same tools we use to analyze the traditional RNA Seq experiment using HiSeq Sequencer. When I say tools, they are FastQC, trimmomatic, STAR (for alignment purposes). My next question is if I could use DeSeq2 package for performing differential gene expression. Would highly appreciate if anyone could tell if there are any important points that I need to keep in mind while analyzing QuantSeq sequenced samples.

Thanks in advance.

Prat