OUTRIDER analysis

OUTRIDER is a package for detecting aberrant expression in RNAseq read count data.

This repository contains a Pipeline to reproduce the results published by Brechtmann et. al.

Project strucure

• This project is setup as a wBuild project with scripts that will be compiled to HTML reports in the Scripts folder.

• Therefore it depends on the packages OUTRIDER and wBuild, which can be obtained from: https://github.com/gagneurlab/

Downloading required data.

• Download the GTEx count table of the V6 release from: GTEx counts

Prereqisite

TODO: This needs to be fixed

git clone https://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/baderda/scared.git OUTRIDER-analysis
cd OUTRIDER-analysis
git checkout PaperAnalysis

and install wbuild using pip by running.

pip install wBuild
wBuild init

then run wbuild init within the cloned repository to initialize the wbuild package.

To run the Paper Pipeline execute the following command.

snakemake 

or to run it on the cluster

snakemake -k --restart-times 4 --cluster "sbatch -N 1 -n 15 --mem 100G" --jobs 16

TODO, what will happen to this??

wbuild init
git checkout readme.md
git checkout Snakefile
git checkout wbuild.yaml

Run the full pipeline

To run the full pipeline please run the following command

snakemake --config DATADIR=Output/data FIGDIR=Output/paper_figures --cores 1 \
        Output/paper_figures/Figure_all_main.pdf -n