This is a Jupyter notebook using Python, R and bash to integrate RNAseq and eCLIP data from ENCODE. It uses an RNAseq data set of KHSRP-shRNA on K562 cells and respective shRNA-mock control. It uses as well an eCLIP data set on KHSRP.
This pipeline comes with a Docker image containing all required software.
You will need to have Docker and git installed.
Start by cloning this repository into your home directory:
cd ~/
git clone https://github.com/mpg-age-bioinformatics/ENCODE_RNAseq_eCLIPThen build the Docker image:
cd ~/ENCODE_RNAseq_eCLIP
sudo docker build -t encode_rnaseq_eclip .Users who wish to run the Jupyter notebook without Docker should install Conda and make sure they have installed Jupyter.
Afterwards one should be able to follow the installation in docker/Dockerfile.
The analysis pipeline was tested on a Docker image running with 8gb of memmory and 4 cpus.
Start your container with:
sudo docker run -d -p 8888:8888 \
-e GRANT_SUDO=yes -e NB_UID=1000 --user root \
-e PASSWORD="YOURPASS" -e USE_HTTPS=yes \
-v ~/ENCODE_RNAseq_eCLIP/notebooks:/home/jovyan/work/notebooks \
-v ~/ENCODE_RNAseq_eCLIP/results:/home/jovyan/work/results \
--name encode_rnaseq_eclip \
-i -t encode_rnaseq_eclipInstead of "YOURPASS" type in a password of your choice.
Then, on your web browser connect to https://localhost:8888.
You will be requested to accepted the self-signed certificate and to give in the password you used in "YOURPASS".
In the Notebook Dashboard navigate to find the notebook: clicking on its name will open it in a new browser tab.
Click on the menu Help -> User Interface Tour for an overview of the Jupyter Notebook App user interface.
You can run the notebook document step-by-step (one cell a time) by pressing shift + enter.
You can run the whole notebook in a single step by clicking on the menu Cell -> Run All.
To restart the kernel (i.e. the computational engine), click on the menu Kernel -> Restart. This can be useful to start over a computation from scratch (e.g. variables are deleted, open files are closed, etc...).
Stop the container with docker stop encode_rnaseq_eclip and restart it with docker start encode_rnaseq_eclip.
The container can be removed with docker rm encode_rnaseq_eclip.
You can remove all images of removed containers with docker rmi $(docker images -q).
MAC users will maybe need to remove the contents of ~/Library/Containers/com.docker.docker/Data/ in order to free space not released after the removal of the images: rm -rf ~/Library/Containers/com.docker.docker/Data/*.