Questions tagged [gtex]

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Applying colocalization analysis in Asian populations

I am planning to add colocalization method as a post-GWAS analysis in my study which is solely based on east Asian populations. I have noticed that coloc, enloc and eCaviar are being commonly used for ...
7-x's user avatar
  • 21
1 vote
1 answer

How to extract column from a matrix matching the another file (sample file)

I have two files master file.txt and sample.txt master.txt ...
Megha's user avatar
  • 395
2 votes
2 answers

How to remove batch effect from TCGA and GTEx data

I want to play some differentially expressed genes for gliomas cancer. I collected cancer tissue profiles from the TCGA database and normal tissue profiles from the GTEx database. I straightforward ...
Kai He's user avatar
  • 21
0 votes
1 answer

Pointing Cromwell to local EBS mounted storage on AWS Batch

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend. I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
Kevin L. Keys's user avatar
1 vote
2 answers

tabix indexing a GTEx variant file- ':' delimited

I have a gtex variant file- the head of which looks as follows: ...
which_command's user avatar
1 vote
1 answer

Is there a single cell RNAseq equivalent of GTEx or TCGA? [closed]

Or do I need to find individual studies and obtain data the long way!
David Peeney's user avatar
1 vote
1 answer

Available phenotype data from GTEx

I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: I would also like to use phenotype data for each sample (especially age, ...
Sylvia Rodriguez's user avatar