(Re)analyses of published RNA-Seq data

This repository contains the files needed for processing and analyzing published RNA-Seq datasets with kallisto and sleuth. The results are hosted at The Lair.

Running an analysis

Assuming you have all of the dependencies installed, the analyses can be run independently with:

snakemake -p --configfile {directory}/config.json

where {directory} should be replaced by a file corresponding to a dataset.

Installation

Using Docker

The easiest way to get this up and running quickly is to use the Dockerfile in the root. This was kindly provided by Konrad Förstner.

To get it up and running, make sure you have docker installed, clone the repository, change to the directory, and fire it up:

git clone https://github.com/pachterlab/bears_analyses
cd bears_analyses
docker build -t lair_test .
docker run -t -i lair_test /bin/bash

This should automatically install all of the dependencies and join the Docker image. You should be able to run the analyses as in section

Manual installation dependencies

If you would like to install everything manually, the dependencies are listed below:

• R (version >= 3.2.1)
• python3 (necessary for snakemake below)
• snakemake which can be installed via pip: pip3 install snakemake
• kallisto
• sleuth devel branch. This can be achieved with devtools in R devtools::install_github('pachterlab/sleuth', ref = 'devel'). Will migrate to the master version soon
• sra-toolkit

License

This code is released under GPLv3. Please see the LICENSE file for more information or visit the Free Software Foundation.