GTEx files, single tissue cis-eQTLs

Question

[Louisa Pyle]

Hi all, I'm using the GTEx analyzed files from single tissue eQTLs at https://www.gtexportal.org/home/datasets . After reading ReadMe, I still don't understand this difference between the eGene file and the significant SNP-eQTL file. I can tell from my analysis that the eGene file is not just a subset of the SNP-eQTL file, and the eGene file for each tissue is significantly smaller. Any insight? LP

Answer 1

[Shicheng Guo]

eGene and significant variant-gene associations based on permutations. The archive contains a *.egenes.txt.gz and *.signif_variant_gene_pairs.txt.gz file for each tissue. Note that the *.egenes.txt.gz files contain data for all genes tested; to obtain the list of eGenes, select the rows with 'qval' ≤ 0.05.

Every SNP-gene association test (including non-significant test). NOTE: This is a very large file and downloading will take hours. If you only need the significant associations, please download the file GTEx_Analysis_v7_eQTL.tar.gz instead. If you need every SNP gene association, but only for a particular tissue, then download the appropriate file in the Tissue-Specific All SNP Gene Associations fileset below.

GTEx input data (Expression Matrix) for FastQTL, if you are not so confident about the downloaded result, you can do it by yourself