So, I was running our day 145 Geoduck data and I had a realization that I applied the coverage cutoff a little early in my data curation. The result of this is I removed potential hypo-methylated sites. Not good. So I re-ran Day 10, 135, and 145 data and the result? More DMLs! Up to 267 from 41 for the Day 10 data. Maybe a good thing in the end? We’ll see.
While I was re-running I looked into potential clustering in the revised Day 10 data. I tried to determine a proper number of clusters through a couple of different methods, but it didn’t look very convincing to me, and the gap statistic method never converged for any values of K between 0 and 100.
notebook entry here: http://rpubs.com/seanb80/250742
Finally, I reorganized my scaphapoda directory on Owl, because it was a nightmare. Geoduck related stuff can now be found in `owl.fish.washington.edu/scaphapoda/Sean/Geoduck_Analysis`. Readme files for the directory and what everything means will be forthcoming!