So last week I was gone, so I was dedicated to knocking a ton of the geoduck stuff out today.
Hollie had asked me to run some ANOVA stuff on the Day 10 and Day 135 samples by treatment. Neither had significant treatment effects, but this is likely due to very small effect sizes being difficult to identify with only 4 samples per treatment group.
I also did a two-way ANOVA looking at both time and treatment for Day 10 and Day 135. That revealed a meaninful time effect, but still no treatment effect.
I also whipped up a bedgraph for the Whole Genome sequencing sample from EPI-135. I thought I had done this while I was gone, but apparently Emu thought differently. Ah well.
The file can be found here.
I then looked at the difference between EPI-135 and EPI-135WG for coverage and a few things. My initial tinkering is here but I’ll likely be playing with it more.
Finally, MethPipe conversion from Bismark bam to whatever special format RADMeth wants for analysis continues. Slowly. Going to leave my laptop running over the next couple does to see if I can hurry it along.