RASflow: RNA-Seq Analysis Snakemake Workflow

RNA-Seq analysis workflow using Snakemake

Workflow

Quick start

Installation

Clone the repository:

git clone https://github.com/zhxiaokang/RASflow.git

Create the environment:

conda env create -n rasflow -f env.yaml

Activate the environment:

conda activate rasflow

Set up configuration

Modify the metafile describing your data configs/metadata.tsv.

Customize the workflow based on your need in configs/config_main.yaml.

Run RASflow

python main.py

Tutorial

A more detailed tutorial of how to use this workflow can be found here: Tutorial

Evaluation

RASflow has been evaluated on 4 datasets including two model organisms (human and mouse) and a non-model organism (Atlantic cod). To keep this repository as light as possible, the evaluation of RASflow on real datasets is deposited here: RASflow_realData

References

RASflow is available as a preprint on bioRxiv: Zhang X, Jonassen I. RASflow: An RNA-Seq Analysis Workflow with Snakemake. bioRxiv. 2019 Nov 839191. Recently accepted by BMC Bioinformatics.