tassel read gwas glm pca gwas mlm - cornell...
TRANSCRIPT
Overview
• Download TASSEL• Read in data• GWAS using GLM• Calculate kinship matrix and conduct PCA• GWAS using MLM• Visualize LD• Cladogram
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Download TASSEL
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www.maizegenetics.net/tassel
Reading in data
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Data > Load > I will make my best guess and try
Fit a generalized linear model (GLM)
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Select “mdp_traits” and “data_hapmap”, and join them together
Fit a generalized linear model (GLM)
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Select “mdp_traits+data_hapmap”, then Analysis > GLM > OK
Make a Manhattan and QQ‐Plot
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Select GLM model results, then Results > Manhattan Plot/QQ Plot
Calculate a kinship matrix
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Select “data_hapmap”, then Analysis > Kinship > Run
Run PCA
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Select “data_hapmap”, then Data > Transform > Create Dataset
Run PCA
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Select “data_hapmap_Collapsed”, then Data > Transform > Impute> Create Dataset
Run PCA
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Select “data_hapmap_Collapsed_3093_imputed”, then Data > Transform > PCA > Create Dataset
Run MLM
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Select “mdp_population_structure”, then Data > Traits > Deselect Q3 > OK
Run MLM
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Join “mdp_traits”, “data_hapmap”, and “Filtered_population_structure”Select merged file and “kin_data_hapmap”, then Analysis > MLM > Run
QQ and Manhattan Plot from MLM
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Investigate LD on Chromosome 1
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Select “data_hapmap”, then Data > Sites > Select Chromosomes
Make an LD Plot
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Select the Chr1 filtered data, then Analysis > Link. Diseq. > Run
Make an LD Plot
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Select the LD data, then Results > LD Plot
Make a Cladogram
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Select the Chr1 filtered data, then Analysis > Cladogram > Run
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Make a CladogramSelect the Tree data, then Results > Tree Plot
Questions?
• Requests for other analyses in TASSEL?
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