the elusive Pop q infile for DISTRUCT

[Caroline]

Dear group:

Alas, I am using CLUMPP and DISTRUCT for the first time.  I understand that DISTRUCT requires a pop Q file as input, which the manual explains is output from STRUCTURE.

I have run STRUCTURE for many projects and have never come across a pop q out put file.  Specifically, I get  as output:

extraparams (txt file)

mainparams (txt file)

PlotData (directory)

Results (directory)

In the results directory, I get individual pop q files for each run. In the plot data - I get the printed estimates of FST, alpha, lnpd. I've seen some discussion of this in other posts, namely, how to make the file (by averaging cluster membership across individuals in each pop), but I'd love to know how to get STRUCTURE to generate it, or, where to find it, if in fact STRUCTURE is generating it.

Thanks!

Caroline

[Vikram Chhatre]

Caroline -

I would recommend using STRUCTURE HARVESTER in your analysis pipeline, between Structure and Clumpp.  It will generate indfiles and popfiles which are to be analyzed separately through CLUMPP.  This will result in two output files, one from each.  Rename the output indfile as name.indivq, and the popfile as name.popq.  Then use those with DISTRUCT plotting.

If you have any specific questions, feel free to post them here.

V

Caroline

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[Caroline]

Hi Vikram,

Thanks for the response. I did in fact use Structure Harvester and it generated the indfile that I used in Clumpp, but no pop file. Here's a zip of the harvester results.  

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[Vikram Chhatre]

Thats interesting.  Harvester must have recently dropped that functionality, since I was just looking at a result archive from October 2012 and it shows output popfiles for CLUMPP.

Dent: Can you confirm that Harvester in fact does not create popfiles anymore?

V

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[Caroline]

Problem solved!   Turns out - in my original input file for Structure, I did not include LocData. Just PopData, which was used by default when I ran the LOCPRIOR model in the absence of LocData. I just re-ran in Structure including the column for LocData, in addition to the column for PopData, and inputed the results into Harvester. Harvester then generated the pop files. Thanks so much!!

C

[Vikram Chhatre]

Indeed. That makes complete sense. Great job catching that error.

---------------------------------------

Vikram Chhatre

Graduate Program in Genetics

Texas A&M University

cryptic...@gmail.com

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[Caroline]

Thx!

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[Dent]

Was drafting a response but it looks like you guys got it worked out. I'll try to add a note to the FAQ about this. Best,

d

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