I made two PCA plots from two types of mappings towards the same genome. In one of them, I allow the reads to just map to one loci, and in the other one I let them map 100 times. After that I do transcript assembly with StringTie in the uniquely mapped reads, and i use the software TEtranscripts for the multi mapped reads (this plot is made just with the gene read counts).
The PCA plots look pretty different: The "unique" mapping separates the two conditions pretty well, and the other one not (not at all). I was wondering if I can still trust the results from the second mapping, or what does this really mean?