Admixture result interpretation
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Entering edit mode
10 months ago
ouyihaoo • 0

Hi All,

I'm currently trying to get the Admixture to work and use it for geographic ancestral inference on my samples. I have able to run Admixture with some 1000 genome data and get the results. However, when I looking into the .Q file it generated, I'm not sure how can I tell which column belongs to which population.

I have run the --cv command and found that K=5 is the right number of populations of my dataset and when I look into the .Q file, it simply shows a table with 5 columns with no header and I'm assuming each row representing 1 sample and it is in the order of my input bed file:

0.919190 0.000010 0.020722 0.008909 0.051169

0.915590 0.000010 0.000010 0.033953 0.050437

0.958658 0.003875 0.001398 0.000010 0.036059

0.957908 0.000010 0.002465 0.032513 0.007104

0.923404 0.000010 0.030266 0.000010 0.046310

0.951790 0.000010 0.010424 0.018024 0.019753

0.932853 0.005237 0.026725 0.000010 0.035175

0.961258 0.000010 0.000010 0.027213 0.011509

I have tried plot the result in a stacked barplot with R and it only shows the composition of each population in each sample by using different color, but still can't tell which color indicating which population/column.

Can anyone help?

Thanks!

genome ancestry ancestry inference admixture • 395 views
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Entering edit mode

Hi ouyihaoo, could you solve the question? Im trying to solve that too. If you could help me I'll appreciate it!

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