I've received data from RNA-Seq from my facility, which was sequenced using QuantSeq Kit. In theory, this kit allows for differential expression analysis cost-efficiently and with lower sequencing depth (less than 10M per sample, in comparison with some samples I got before, which had 30-35M per sample). The paper is here: https://www.nature.com/articles/nmeth.f.376.pdf
I know that, in addition to sequencing depth, we should also be looking into the experimental design in order to increase my statistical power. However, I found some one workflow designed for QuantSeq data especifically.
My question is if any of you have experience with QuantSeq data and know if it's possible to use DESeq2 directly in the data produced?
Thanks in advance!