Answer to Part 1.1: Is there an intrinsic reason on why the GC content RNAseq (cDNA) sequences would violate your genome-wide expectations (besides adapters)? (-0.25)
Answer to Part 2: Are you sure only 15 samples pass the suggested unique-read cutoff? Are you sure there's no inconsistent structure within replicates? (-0.5)
Otherwise I have no complaints. Good job!
Code: 4.5/4.5 Answers: 2.75/3.5 Plots: 2/2 Report: 0/1 Total: 9.25/11