Post date: Oct 10, 2014 8:2:12 PM
#10Oct14: First I noticed I am missing the SI afreq files for both chains in /Volumes/data/stygoparnus/sims. So, I emailed Kate to see if they just didn't get transferred from the cluster she ran this on. I'm waiting to hear back... Kate transferred them over, changed the permissions. All Stygoparnus afreq files are now in:
/Volumes/sims/lkl/stygoparnus/afreq_HighCov/
#14Oct14: Used R script called theta_fig_14oct14.R to get theta point estimates and 95% CIs for each Stygoparnus population. Stygoparnus thetas are way higher than the other three taxa. Could this be merely because I have 191,679 SNPs for 53 individuals in this dataset vs. only hundreds or thousands of SNPs for the other datasets?
I also used the R script called stygoparnus_PCA_14oct14.R to get PCA infiles and do a PCA. The first 6 PC's at least explain just about the same amount of variation (weird?). Also, the Stygoparnus PCA looks different from the other three taxa. What to think?