Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
Creators
- Caudal, Elodie (Project member)1
- Loegler, Victor (Project member)1
- Dutreux, Fabien (Project member)1
- Vakirlis, Nikolaos (Project member)1
- Teyssonnière, Elie (Project member)1
- Caradec, Claudia (Project member)1
- Friedrich, Anne (Project member)1
- Hou, Jing (Project leader)1
- Schacherer, Joseph (Project manager)1, 2
- 1. Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- 2. Institut Universitaire de France (IUF), Paris, France
Description
Scripts used in the Paper "Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast" for RNA seq and GWAS analyses.
# TPM calculation
TPM were calculated using the R script `tpm_calc.R`.
# GWAS
The script `simpleGWAS2_VV_Template.sh` is a template script to run a genome wide association between genotypes and phenotype in a single condition. It requires FaST-LMM 0.6.4 and R with qqman, viridis and stringr packages. It requires the scripts `rank_based_Inverse_Normal_Transformation.R` to normalize phenotypes, `runFaSTLMM.py` to run the associations, `calc_GIF.R` to compute the Genomic Inflation Factor and `qqman_script.R` to generate the Manhattan and QQ plots.
The script `runParallel.sh` can be used to run multiple association in parallel. Just fill the 7 top variable and the `simpleGWAS2_VV_Template.sh` script will be filled and launched multiple times in parallel.
Files
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