faststructure distruct popfile

[Liliam Martinez]

Hi:

So, I ran structure for K=2 to K=10, then ran chooseK.py and chose the optimal range of K. How do I generate the popfile of distruct?. I already read about it in https://github.com/cryptic0/distruct2 but honestly I can't understand how to generate the popfile from my data. My optimal K=3 to 5 and I want to get the distruct plot for those K. How do I generate my popfile from these data? (This is my meanQ file output)

 

0.651313	0.000018	0.037936	0.06268	0.248053
0.35459	0.000018	0.000018	0.645356	0.000018
0.000017	0.000017	0.000017	0.000017	0.999932
0.999927	0.000018	0.000018	0.000018	0.000018
0.000018	0.999927	0.000018	0.000018	0.000018
0.000023	0.000023	0.000023	0.627159	0.372771
0.000017	0.000017	0.000017	0.000017	0.999932
0.000018	0.000018	0.000018	0.000018	0.99993
0.000017	0.999924	0.000017	0.000017	0.000025
0.000018	0.000018	0.000018	0.000018	0.999927
0.000018	0.916303	0.000019	0.046466	0.037194
0.000017	0.000017	0.000017	0.000017	0.999931
0.000018	0.000018	0.000018	0.226369	0.773577
0.355848	0.000018	0.000018	0.000018	0.644099
0.000017	0.083603	0.000017	0.916346	0.000017
0.000017	0.999933	0.000017	0.000017	0.000016
0.000017	0.000017	0.000017	0.000017	0.999932
0.000017	0.000017	0.000017	0.999932	0.000017
0.000017	0.107467	0.000017	0.000017	0.892482
0.000031	0.248757	0.000017	0.751178	0.000017
0.000022	0.139684	0.000017	0.86026	0.000017
0.000017	0.999933	0.000017	0.000017	0.000017
0.000017	0.000017	0.000017	0.000017	0.999931
0.000025	0.140855	0.000017	0.818591	0.040512
0.000021	0.454389	0.000021	0.000021	0.545548
0.00002	0.00002	0.00002	0.00002	0.999921
0.000017	0.999933	0.000017	0.000017	0.000017
0.000017	0.000017	0.000017	0.000017	0.999932
0.000018	0.078914	0.000018	0.000018	0.921031
0.000017	0.904865	0.000017	0.000017	0.095083
0.000017	0.011895	0.000017	0.000017	0.988054
0.000017	0.977358	0.000017	0.000017	0.02259
0.000017	0.000017	0.000017	0.000017	0.999932
0.000019	0.000019	0.000019	0.000019	0.999926
0.392674	0.00002	0.00002	0.00002	0.607267
0.00006	0.208746	0.091919	0.151379	0.547896

Thanks a lot!

[Vikram Chhatre]

Liliam,

I recommend against using that version of distruct from github; there are notes on github to that effect.  I have updated that script and it has been moved back to my website.  http://distruct2.popgen.org.

As for popfile, it contains just a list, one column, with one row per individual, filled with population id.  For example:

pop1

pop1

pop1

pop2

pop2

pop3

pop3

pop3

The distruct2 archive should have example files.

V

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[Liliam Martinez]

Yes but how can I get those for my data?. I mean how do I know which ones belong to which population?.

Thanks!

Liliam

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[Vikram Chhatre]

You can choose to not include a popfile, but then your plot will be sorted by K.

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[Liliam Martinez]

Well but I would really like to sort my data by population. How can I get which individuals belong to a specific population so I can create my popfile?

Thanks

Liliam

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[Vikram Chhatre]

A 'population' can be an arbitrary designation that we assign to individuals depending upon how we collected samples.  

'K' is also a population, but not arbitrarily assigned.  It is a genetic cluster inferred from allele frequency data where individuals within a given K cluster more or less conform to HWE.

V

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[Liliam Martinez]

ok, but you do need a poporder file for distruct2 right?. How can you create the poporder file?. If you have K=5 that means you have "pop1, pop2, pop3, pop4 and admixed" or "pop1, pop2, pop3, pop4, pop5 and admixed"

thanks!

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[Vikram Chhatre]

The only reason to use distruct2 instead of the original distruct that comes with fastSTR is to be able to order populations.  If you don't need that functionality, use the original script.  An example for poporder file is provided with the script.

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[Liliam Martinez]

Thanks for all your help but I still need to solve something. I already managed to produce the plots and they look great. I already ran chooseK and I got the optimal K range. I have 264 genotypes from the same specie but different subspecies and I would like to know which individuals were assigned to each cluster.

Thanks for your patience!

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[Otyama Paul]

Hi Liliam Martinez,

Did you ever find a solution to your problem? I want to do the same thing but don't know how to go about it. I simply want to know which individuals were assigned to each cluster without having to manually call them (which can be tedious and error prone but above all not replicable)

Thanks,

Paul