kew24 / rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

Bulk RNAseq Workflow

• Bulk RNAseq Workflow
  • Usage
    • Step 1: Configure the workflow
    • Step 2: Test and run the workflow

Usage

NOTE this workflow is optimized for the HPC @ Van Andel Institute.

Step 1: Configure the workflow

• Move your sequencing reads to raw_data/

• Modify the config and samplesheet:

  • config/samplesheet/units.tsv; To make a template based in the files in raw_data/, run ./make_units_template.sh.

    • sample - ID of biological sample; Must be unique.
    • group - Experimental group
    • fq1 - name of read1 fastq
    • fq2* - name of read2 fastq

  • config/config.yaml

Step 2: Test and run the workflow

Test your configuration by performing a dry-run via

snakemake -npr

Execute from within your project directory as a SLURM job.

sbatch bin/run_snake.sh