Snakemake workflow: RNAseq_kadal

A snakemake workflow to analyze gene expression in tail regeneration of G. gecko. This workflow was build using the snakemake cookie-cutter template and heavily inspired by this workflow.

Authors

• Luthfi Nurhidayat
• Roxane Boyer
• Matin Nuhamunada

Workflow overview

Usage

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above).

Step 1: Obtain a copy of this workflow

Clone this repository to your local system, into the place where you want to perform the data analysis. Make sure to have the right access / SSH Key.

git clone git@github.com:matinnuhamunada/rnaseq_kadal.git
cd rnaseq_kadal

Step 2: Configure workflow

Configure the workflow according to your needs via editing the files in the config/ folder. Adjust config.yaml to configure the workflow execution, samples.tsv, and units.tsv to specify your sample setup.

The parameter samples denote the location of your .tsv file which specify the samples to analyse. The parameter units informs the paired end .fastq locations of each sample.

Example : samples.tsv

Example : units.tsv

Step 3: Install Snakemake

Installing Snakemake using Mamba is advised. In case you don’t use Mambaforge you can always install Mamba into any other Conda-based Python distribution with:

conda install -n base -c conda-forge mamba

Then install Snakemake with:

mamba create -c conda-forge -c bioconda -n snakemake snakemake

For installation details, see the instructions in the Snakemake documentation.

Step 4: Execute workflow

Activate the conda environment:

conda activate snakemake

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

or

snakemake --use-conda --drmaa --jobs 100

If you not only want to fix the software stack but also the underlying OS, use

snakemake --use-conda --use-singularity

in combination with any of the modes above. See the Snakemake documentation for further details.

Step 5: Investigate results

After successful execution, you can create a self-contained interactive HTML report with all results via:

snakemake --report report.html

This report can, e.g., be forwarded to your collaborators.