This is a fork of RiDE (RNA Differential Expression), a Snakemake-based pipeline for Next-Generation Sequencing RNA-Seq differential expression analysis, developed at CRS4 Next Generation Sequencing Core Facility. Software dependencies are directly managed by Snakemake using Conda, ensuring the reproducibility of the workflow according to FAIR principles.

• Clone the repository from git-hub:

git clone https://github.com/igg-bioinfo/ride.git

• Rename the folder, from ride to your PROJECT_NAME:

mv ride PROJECT_NAME

• cd into the newly created folder:

cd PROJECT_NAME

• Edit the configuration files in conf subfolder:

  • config.yaml - paths to your reference files: genome, target regions, etc.
  • samples.tsv - associate samples to FASTQ files
  • units.tsv - paths to FASTQ files

• Edit the Snakefile and uncomment the output files you need

• If conda package manager is not available, install miniconda.

• Create a virtual environment containing snakemake, as suggested here. First install mamba as a replacement of the default conda solver:

conda install -c conda-forge mamba

• Then, install snakemake:

mamba env create --name snakemake --file environment.yaml

• Activate the enviroment:

conda activate snakemake

• Run snakemake in dry-run mode to check if everything is fine. YOUR_WORKING_DIR could follow the format: YYYY-MM-DD.

snakemake --cores 32 --use-conda --configfile conf/config.yaml --printshellcmds -d YOUR_WORKING_DIR --rerun-incomplete --keep-going --dryrun

• For verbose output:

snakemake --cores 32 --use-conda --configfile conf/config.yaml --printshellcmds -d YOUR_WORKING_DIR --rerun-incomplete --keep-going --verbose --reason --dryrun

• If you are happy with the --dryrun, run snakemake:

snakemake --cores 32 --use-conda --configfile conf/config.yaml --printshellcmds -d YOUR_WORKING_DIR --rerun-incomplete --keep-going

Tip: For large projects, we suggest to run snakemake in a screen session.