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? There's some inconsistent structure within replicates, but you should see, for the most part, triplicate blocks at lower thresholds. (-0.5)
Heatmap: Missing replicates for each tissue (-0.5)
Code: 4.5/4.5 Answers: 2.75/3.5 Plots: 1.5/2 Report: 1/1 Total: 9.75/11