Question: GTEx files, single tissue cis-eQTLs
2
gravatar for Louisa Pyle
2.7 years ago by
Louisa Pyle20
Philadelphia, PA, US
Louisa Pyle20 wrote:

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

gtex eqtl • 1.6k views
ADD COMMENTlink modified 14 months ago by Shicheng Guo8.1k • written 2.7 years ago by Louisa Pyle20
0
gravatar for Shicheng Guo
14 months ago by
Shicheng Guo8.1k
Shicheng Guo8.1k wrote:

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

ADD COMMENTlink modified 14 months ago by RamRS26k • written 14 months ago by Shicheng Guo8.1k
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