Some small corrections for chapter 4, and missing figures in HTML version.

[pfh]

4.3
"The gene annotation files were obtained as GFF files from RefSeq and used that to construct"
Remove "that".

4.3
"$log_2$"
-> $\log_2$

4.3
"For each gene, the weighted mean and standard deviation of the log-transformed coverage score were computed over all intron and exon parts within the groupings of genotype and line."
From your code I see this is weighting by width, but it wasn't obvious to me when reading your thesis.

4.3
"(ref:si-upset)"
Weird bit of code that appears in HTML version.

4.3
PDF format figures do not appear in HTML version.

Why do the coverage plots have slashed lines /// ?

4.4
"We have shown how to coverage can be"