I performed a WGS with Illumina on three histological sections. I looked for viral genomes and I got one hit for Epstein-Barr virus. Then I performed PCR to confirm the data and I got an unclear result for the sample positive by WGS and two positives for the other two samples.
How shall I consider this analysis? That the WGS was garbage? Is there a way that PCR and WGS could give different values? for instance, the sections were different...