Post date: Feb 13, 2017 4:33:50 PM
Back in November I re-ran popanc on the 13 admixed Lycaeides populations with 3 and 7 bp windows (+-) for the LDA part of popanc. These runs were with L. anna and L. melissa (west) as reference populations and included analyses of autosomes and sex chromosomes. All previous runs were deleted or moved to 'old' sub-directories; 5 bp window parameter estimates are in /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/ancfreqs/params/window5. I summarized admixture proportions (popQ) and local ancestry with estpost:
perl runEstpost.pl out_w*0.hdf5
The q and z parameter estimate files are in /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/ancfreqs/params/.
Running initial analyses in the results sub-directory based on 3 bp window size. "Finished" running through R script and saved Rdat is current. Need to dig in more.