Sam’s Notebook: DNA Methylation Analysis – Olympia Oyster Whole Genome BSseq Bismark Pipeline MethylKit Comparison

0000-0002-2747-368X

I previously ran two variations on the Bismark analysis for our Olympia oyster whole genome bisulfite sequencing data:

• 20180913 Bismark tweaks

I followed this up using the MethylKit R package to identify differentially modified loci (DML), based on differing amounts of coverage (1x, 3x, 5x, & 10x) and percent methylation differences between the two groups of oysters (25%, 50%, & 75%).

See the project wiki for experimental design info).

Both sets of analyses were documented in R Projects:

Default Bismark settings:

• 20180912_oly_methylkit (GitHub)

“Relaxed” Bismark settings

• 20180913_oly_methylkit