PCAngsdTutorial: Difference between revisions
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===Set paths=== | ===Set paths=== | ||
Every time you open a new terminal window, set the paths to the program and the input file. | |||
Set the path to PCAngsd | ===Set the path to PCAngsd=== | ||
<code> | |||
PCAngsd=~/Software/PCAngsd | |||
</code> | |||
Test the link | Test the link | ||
ls $ | <code> | ||
ls $PCAngsd | |||
</code> | |||
Set the path to the input file, for example: | |||
Download and Set the path to the input file, for example: | |||
'''*ANDERS*''' | |||
cd | |||
wget popgen.dk/software/download/NGSadmix/data/input.gz | |||
maybe change it to: | |||
wget popgen.dk/software/download/PCAngsd/data/input.gz | |||
GL1000Genomes=./input.gz | |||
'''*ANDERS*''' | |||
Revision as of 22:40, 29 July 2019
We will go through a simple and more complex example on how to use PCAngsd with visualization of the data.
PCA with admixture aware priors
This example will perform a PCA analysis on 1000 genotype likelihoods.
Set paths
Every time you open a new terminal window, set the paths to the program and the input file.
Set the path to PCAngsd
PCAngsd=~/Software/PCAngsd
Test the link
ls $PCAngsd
Download and Set the path to the input file, for example:
*ANDERS*
cd wget popgen.dk/software/download/NGSadmix/data/input.gz maybe change it to:
wget popgen.dk/software/download/PCAngsd/data/input.gz
GL1000Genomes=./input.gz
*ANDERS*