3.3.3 QuantSeq versus whole mRNA-Seq
We compared the gene expression of the same 14 blood samples (Ntot=28) among RNA-Seq libraries built using QuantSeq and NEB. We found 15,328 out of 26,316 genes (58%) that were significantly (adjustedp -value <0.05) differentially expressed among library types (Table S2 on Dryad). Specifically, we found 9852 (64%) transcripts with higher expression in NEB versus QuantSeq and 5476 (36%) transcripts with higher expression in QuantSeq versus NEB. Within sampling methods, the percentage of differentially expressed genes between QuantSeq and NEB was 45%, 41%, and 44% for dip netting, electrofishing sampled immediately, and electrofishing sampled after 5 min, respectively (Table S2 on Dryad). The proportion of identical genes with differential expression favoring one of the two library methods is very similar, although does favor NEB with increased transcript length (Figure 5). Log of the basemean expression differences for NEB relative to QuantSeq was only 0.098 for transcripts <1000 bp, but was 0.27 for transcripts between 5000-6000 bp (Figure 5).