An automated pipeline for eQTL detection and downstream analysis
Make sure you have istalled Docker and Docker Compose.
sudo apt install docker .io
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
wget https://github.com/diegommartinezr/eQTL_Detector/archive/master.zip
sudo usermode -aG docker ${USER}
And then
su - ${USER}
This last step is going to ask you for your su passwoed
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
After you have all the data on the Bed-Seq folder to run the pipeline just run the follow command:
bash Run_Pipeline.sh