I am new to cuff diff and just got my data output back and it doesn't look
like anything is statistically significant. There are three treatment
groups with two biological replicates each group. I am not sure if I made
an error somewhere along the line, need to adjust the parameters, or if
there really could be no change. The samples are from sheep and I have been
using the OvisAries3.0 reference I downloaded from UCSC.

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