Input files - eQTL

[gpwhiz]

I had couple of quick questions. I found a word doc tutorial from you which mentions which files to use as eQTL input. In your document, you mention that there are two files in the <all.pairs.txt.gz>. But I found there is only a single file, with the following headers gene_id	Variant ID	tss distance	ma_sample	ma_count	maf	pval_nominal	slope	slope_se

Is this is correct file. The folder GTEx_Analysis_v7_eQTL.tar.gz that has two files and these files are called Tissue.v7.egenes.txt.gz and Tissue.v7.signif_variant_gene_pairs.txt.gz Which files should I be using??

[kevinblighe]

That depends on what analysis you want to conduct.