Help making ADMIXTURE output digestible

Question

[devenvyas]

I am new to the program ADMIXTURE.

I am running it from K=1 to K=20 on a set of 2033 individuals and 276,899 SNPs post-LD-pruning. The sample order is based on the default order in the dataset I downloaded, so population members are not necessarily back-to-back and related populations are not necessarily listed near each other.

Ideally, in the morning I will have a set of 40 *.Q files (20 with CV and bootstrap and 20 without), so in preparation I am trying to figure out how to graph them with the bars in a meaningful order. I was wondering if anyone had suggestions on how to this (or general suggestions about managing ADMIXTURE output).

Thanks!

[beausoleilmo]

I have the exact same question! Here is a similar one: Can't figure out order of output rows in ADMIXTURE

Answer 1

[beausoleilmo]

I found this website explaining how to do the full analysis. Basically, you have to look in the .fam file. You can import this file in R like this: fam = read.table("~/path-to-the-file/my_analysis.fam"). After that I was reusing the first column and rename the rows of your .Q file: tbl = read.table("~/path-to-the-file/my_analysis.Q"). Use this dataset to print your barplot!

[dr.fakharunnisa]

Hello i was looking for the same question. I found multiple unanswered posts over this. Thank you for your answer but i am unable to reach the link provided by you 'this website'. you may please guide again. Thank you

[beausoleilmo]

I updated the website to this: https://www.discovermagazine.com/the-sciences/analyzing-ancestry-with-admixture-step-by-step. Seems to work.

[dr.fakharunnisa]

Thank you. I will check it out