eQTL_Detector

An automated pipeline for eQTL detection and downstream analysis

Before start

Make sure you have istalled Docker and Docker Compose.

Install Docker

sudo apt install docker .io

Install Docker-Compose

Firt download Docker-Compose

sudo curl -L https://github.com/docker/compose/releases/download/1.21.2/docker-compose-`uname -s`-`uname -m` -o /usr/local/bin/docker-compose

Give chmod to the application

sudo chmod +x /usr/local/bin/docker-compose

Finally check the version

docker-compose --version

If everything is fine you should see something like this:

docker-compose version 1.21.2, build a133471

Download this repository

wget https://github.com/diegommartinezr/eQTL_Detector/archive/master.zip

In case you have the usermode issue you need to use

sudo usermode -aG docker ${USER}

And then

su - ${USER}

This last step is going to ask you for your su passwoed

Preparing your Data

This pipeline use three different data:

• Genotyping data in .VCF format
• RNA-Seq data in .BAM format
• A covariance matrix in .txt format

Appart from the source data the reference data to use will be:

• Annotations in .BED format
• A .GTF file containing the gencode annotation

Put all these files on the Bed-Seq folder and you will be ready to go

Running the pipeline

After you have all the data on the Bed-Seq folder to run the pipeline just run the follow command:

bash Run_Pipeline.sh