High %Dups after cut adapt

Question

[smithkthedale]

Hi,

So I extracted RNA Seq from 50 plant tissues (3 replicates of each type of tissue) and 51 out of the 53 samples have about an 60% - 80% %dups.

For example, here is one samples data:

Forward Strand: 81.5% dups 43% GC 65.9 MSeqs 
Reverse Strand: 73.8% 42% GC 65.9 MSeqs 

but then I have two out of the 50 samples I sequenced that are way far off. For example, some sample is

Forward Strand: 37.0% dups, 43% GC, 1.4 MSeqs 
Reverse Strand : 33.0% dups, 41% GC, 1.4 MSeqs 

Is this bad data? What could be wrong with it?