FastStructure:ChooseK

[Vinod Kumar]

I am running faststructure for a SNP dataset and whatever I am assuming k=3, k=5, k=10, k=15 but chooseK command returning the same likelihood and structure in data. I've assumed and detected 8 populations through PCA. I am running the following command 
python structure.py -K 15 --input=finalpruned1 --output=genotypes_finalpruned_15

What should I do or I am doing wrong in estimating final pop through chooseK command?

Thanks,

Vinod Kumar

[Vikram Chhatre]

Can you post the chooseK command you are using?

V

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[Vinod Kumar]

I have run the default command mentioned in the tutorial without changing anything.

[Vikram Chhatre]

You are running chooseK.py on a range of K values, right?  If yes, can you post the output here?

V

[Vinod Kumar]

Sorry Vikram Chhatre for very late response.

First I have run main script (data is in bed, bim and fam format) ()

$ python structure.py -K 20 --input=genotypes --output=genotypes_finalpruned_20

After this I have run this script  to choose the appropriate number of model components that explain structure in the dataset

$ python chooseK.py --input=genotypes_finalpruned_20

Results of this command are

Model complexity that maximizes marginal likelihood = 20
Model components used to explain structure in data = 20

I am also attaching the output of the faststructure.

am I doing something wrong to asses structure in my dataset or this mean my data doesnt have any structure? or I am missing something.

Thanks,

Vinod Kumar

PostDoc Fellow,

International Wheat Genome Sequencing Consortium (IWGSC),

NRC on Plant Biotechnology,

Indian Agricultural Research Institute,

New Delhi-110012

[Vikram Chhatre]

ChooseK needs results from a range of K values.  Also, the -K 20 flag for fastStructure will only test K=20.  

1. Run fastStructure K1 through Kn (multiple runs are to be set manually)

2. python chooseK.py --input=prefix_for_all_K_runs

[Vinod Kumar]

Thanks a lot Vikram for the valuable answer. I have run only k=20 but now I will run for all the K and then will run the chooseK script.

Thanks,

Vinod Kumar

[Hilçana Albuquerque]

Good Morning

I'm trying to visualize which individuals belong to each group but I'm not sure how to find this information.

can anybody help me?

Example: Grp Genotype

                  1 1,2,3,4,5,6

                  2 10,11,12,13