GitHub-GTEx Pipeline- how to execute ?
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3.6 years ago
David_emir ▴ 390

Hello Guys,

I am interested on getting Correlations between genotype and tissue-specific gene expression levels. I am trying to replicate the same analysis pattern which was described in This Paper. I have also came across the following pipeline in gitHub GitHub-GTEx Pipeline, but i am not able to run this pipeline. My knowledge about scripts is less than that of a Beginner and i am a Biologist (Healthcare dept) and this script look too complicated for me to understand, I request you guys to help me (Tutorials) in executing this pipeline i have around 20 .fastq files (paired end). I would love to see the co-relations. Please help.

Thanks a lot for your kind help, Have a great day !!! Dav.

GTEx pipeline execution rna-seq genotype • 2.0k views
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Just a comment - this is a BroadInstitute core pipeline, which means that it is created to be implemented by people with advanced bioinformatics skills. From a quick first look, I see WDL and docker involved - I would not recommend tackling WDL as your first foray into bioinformatics, but I might be mistaken on its target audience. Wait for others' inputs and see how you can take this forward.

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The Broad WDL tutorial/docs seem to be written for newcomers with minimal programming experience, so you should be fine trying it out.

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Here's a new post that gave me some insight into WDL execution: Problem parsing interval list file to GenomicsDBImport in GATK4

Turns out, cromwell can execute WDL scripts. I'd say combine reading the WDL tutorial - same link as earlier along with the cromwell tutorial to gain an understanding of both.

Exciting stuff! Love where we're headed!

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we have published the GTEx RNA-Seq pipeline on the Truwl platform (sorry maybe 3.4 years too late for you)

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