Sean’s Notebook: C. virginica MACAU results.
So I finished running MACAU on the C. virginica oil spill samples a couple of different ways. First, I ran all 6 samples, 3 control and 3 oil exposed and secondly, 2 control and 3 oil exposed. The difference being one of the samples had really low read counts from the sequencing facility, and that brought down the number of available loci with a minimum of 10x coverage to look at from ~70,000 to ~17,000
Neither produced many loci that had meaningful priors, the 6 sample run had 4, and the 5 sample had 16. None had meaningful predictor parameters (beta), meaning that oil exposure was not a significant predictor of methylation status. After talking to Steven, this is not surprising, as other recent studies have shown similar lack of differentially methylated regions/loci.
Also, I’ve started revamping the Hyak wiki, trying to chunk it out to make it a little more readable by the average person. It’s on my personal Github wiki at the moment, but I will copy it over once I got some input on formatting and a few things.