From ceae21b4d1291241c6aad4ee88ace28653c2a548 Mon Sep 17 00:00:00 2001 From: Atemia <j.atemia@fz-juelich.de> Date: Wed, 4 Dec 2024 16:49:21 +0100 Subject: [PATCH] chore: restructure directories and relocate final cleaned GWAS data --- .../README.md | 23 +++++++++++++++++++ .../protocols/.gitkeep | 0 .../resources/.gitkeep | 0 .../genotype/README.md | 3 +++ .../all_taxa_3455_accessions.hapmap.txt | 3 +++ .../diplo_per_geno_3455_accessions.hapmap.txt | 3 +++ ...s_perennis_geno_3455_accessions.hapmap.txt | 3 +++ .../hue_geno_3455_accessions.hapmap.txt | 3 +++ .../lux_geno_3455_accessions.hapmap.txt | 3 +++ ..._plus_nica_geno_3455_accessions.hapmap.txt | 3 +++ ...mex_chalco_geno_3455_accessions.hapmap.txt | 3 +++ ...ex_durango_geno_3455_accessions.hapmap.txt | 3 +++ .../mex_geno_3455_accessions.hapmap.txt | 3 +++ .../genotype/mex_hapmap_101.txt | 0 ...sa_central_geno_3455_accessions.hapmap.txt | 3 +++ ...x_nobogame_geno_3455_accessions.hapmap.txt | 3 +++ 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studies/processed_genotype_phenotype_teosinte_data/resources/gwas_data_3455_accessions/phenotype/plink_fomart/parv_pheno.csv create mode 100644 studies/processed_genotype_phenotype_teosinte_data/resources/gwas_data_3455_accessions/phenotype/plink_fomart/parv_pheno_plink.txt create mode 100644 studies/processed_genotype_phenotype_teosinte_data/resources/gwas_data_3455_accessions/phenotype/plink_fomart/per_pheno_plink.txt diff --git a/studies/processed_genotype_phenotype_teosinte_data/README.md b/studies/processed_genotype_phenotype_teosinte_data/README.md new file mode 100644 index 0000000000..14f99526b7 --- /dev/null +++ b/studies/processed_genotype_phenotype_teosinte_data/README.md @@ -0,0 +1,23 @@ +# GWAS Data for Teosinte Taxa + +This directory contains cleaned and finalized data files for conducting a Genome-Wide Association Study (GWAS) on **3,455 individuals** spanning all seven teosinte taxa. +The dataset includes climate, morphological, and genetic data, and is subsetted by taxa for targeted analyses. + +## Directory Structure + +## [Resources](`resources/gwas_data_3455_accessions`) + +### Key Files + +- **`all_taxa`** + Contains GWAS-ready data for all 3,455 teosinte individuals, combining climate, morphological, and genetic datasets. + +- **`taxa_specific`** + Subsetted GWAS-ready data files for each of the seven teosinte taxa: + - _Zea mays ssp. parviglumis_ + - _Zea mays ssp. mexicana_ + - _Zea diploperennis_ + - _Zea mays ssp. huehuetenangensis_ + - _Zea luxurians_ + - _Zea nicaraguensis_ + - _Zea perennis_ diff --git a/studies/processed_genotype_phenotype_teosinte_data/protocols/.gitkeep b/studies/processed_genotype_phenotype_teosinte_data/protocols/.gitkeep new file mode 100644 index 0000000000..e69de29bb2 diff --git a/studies/processed_genotype_phenotype_teosinte_data/resources/.gitkeep b/studies/processed_genotype_phenotype_teosinte_data/resources/.gitkeep new file mode 100644 index 0000000000..e69de29bb2 diff --git 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