PopStructure_PipelineNotes.txt

## Notes on Structure/Tess to visualization pipeline



# 1 Structure  http://pritch.bsd.uchicago.edu/software.html

run analysis

# 2 Structure harvester

2 options: a. online or b. on personal machine

  a. online: http://taylor0.biology.ucla.edu/structureHarvester/
	upload zipped "results" folder from structure run
	Harvester will output files for chosen K as well as to run through distruct

  b. on personal machine (occasionally harvester website is down)
	download and compile python code
	run for same result as a.
	
  Next, run Clumpp to combine replicate runs
  	run clumpp (available at http://www.stanford.edu/group/rosenberglab/clumpp.html ) on structure results to compile replicate runs
  	edit the paramfile directly or use code below
  	make popfile
	  	./CLUMPP paramfile –p population input file, output from harvester –o designate output file –k # of clusters –c number of populations –r number of chains (reps)
		  **NB In paramfile, change datatype to ‘1’ to designate population file
	  make indfile
		  ./CLUMPP paramfile –i individual input file, output from harvester –o designate output file –k # of clusters –c # of individuals –r # of chains
		  **NB In paramfile, change datatype to ‘0’ to designate individual file
	
# 3 distruct

program available at: http://www.stanford.edu/group/rosenberglab/distruct.html

the above procedures will produce a popfile and an indfile for each K
read these into distruct and run:
	./distructMacOSX1.1 –K # clusters –M # pops –N # individuals –p population input file –i individual input file –o designate output file
	
	edit the drawparams file for visual settings
	choose colors in "casia.perm"
	designate names in "casia.names"


# 4 Tess   http://membres-timc.imag.fr/Olivier.Francois/tess.html

Tess has an option to directly output a clumpp file from runs for each K
Do this then follow steps 2 and 3 above