I recently did a cuffdiff to estimate differential expression under two different conditions. I did not have replicates for the data-sets. I used tophat2 and cuffdiff2 for alignment and differential expression respectively. However, most strangely, when I viewed the alignment on IGV, I can see four genes where the coverage is decent, but the FPKM table shows a value of zero in both conditions. Now I should say, that these genes are tandemly repeated. However, when I tried to look for other repeat regions in the genome, they had some FPKM value assigned to it. I wonder what is going on.