Transposons are a major contributor to gene expression variability under selection in rice populations

Dataset and code related to the publication: 

Castanera R., Morales-Díaz N., Gupta S., Purugganan M., Casacuberta JM (2022). Transposons are a major contributor to gene expression variability under selection in rice populations. Research Square. https://doi.org/10.21203/rs.3.rs-2197876/v1. 

1) TIP_data folder: 

INDICA_teinsertions_5_2_2_matrix_sorted_ID_MAF003.txt: TIP matrix used for TIP-eQTL mapping (binary form, where 0 = absence, 1= presence)
INDICA_teinsertions_5_2_2_matrix_sorted_ID_MAF003.info: TIP information (chrom,start,superfamily,family,maf)
JAPONICA_teinsertions_5_2_2_matrix_sorted_ID_MAF003.txt: TIP matrix used for TIP-eQTL mapping (binary form, where 0 = absence, 1= presence)
JAPONICA_teinsertions_5_2_2_matrix_sorted_ID_MAF003.info:TIP information (chrom,start,superfamily,family,maf)

2) SNP_data folder: 

SNP_matrix_final_IRGC_Indica_MAF003.lfmm: SNP binary matrix used for TIP-eQTL mapping 
SNP_matrix_final_IRGC_Indica_MAF003.info: SNP information
SNP_matrix_final_IRGC_japonica_MAF003.lfmm: SNP binary matrix used for TIP-eQTL mapping 
SNP_matrix_final_IRGC_japonica_MAF003.info:SNP information

3) Expression data: 

Normalized expression data and accessory files used for TIP-eQTL analysis (as described in TIP-eQTL_matrix.R)

Code:

PopoolationTE2.sh: Bash script to reproduce PopoolationTE2 analysis (TIP detection)

TIP-eQTL_matrix.R: R code to reproduce eQTL analyses