Answer to Part 1.1: Is there an intrinsic reason on why the GC content of RNA-seq (cDNA) sequences would violate your genome-wide expectations for the first few nucleotides? (-0.25)
Answer to Part 2: Are you sure none pass the suggested unique-read cutoff? Are you sure there's no inconsistent structure within replicates? (-0.5)
Answers to Part 3: Are you sure the clustering step was done properly? I suspect some issues with the gene cluster may be causing your skewed observations of GO.
Code: 4.5/4.5 Answers: 2.75/3.5 Plots: 2/2 Report: 1/1 Total: 10.25/11