I have two datasets from different sources. Unfortunately one group have done unstranded RNA-seq while the second one has done stranded. When I do the PCA analysis of normalized reads using DESeq2, I see them clustering far from each other. Now I am doubtful if there is an artefact coming from the unstranded reads of the first group or is the difference real. Could anyone enlightment me if it would be appropriate to use these two datasets for comparisons for differential gene expression or will get wrong information for transcripts on the reverse strand?