RNA-Seq Analysis

Input data

Dataset: Demultiplexed fastq fileset sample GCF-MB-7361_pool18RNA from flowcell HC232DRX3 on 2023-05-23 #1

Base workflow

snakemake-workflows/rna-seq-star-deseq2

Setup and configuration

Refer to the Snakemake Workflow Catalog for more detail

1. install Snakemake and Snakedeploy

mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
conda activate snakemake

2. deploy workflow

mkdir -p path/to/project-workdir
cd path/to/project-workdir
snakedeploy deploy-workflow https://github.com/snakemake-workflows/rna-seq-star-deseq2 . --tag v2.0.0

Consider putting this directory under version control.

3. configure workflow

   • config/config.yaml

   • config/samples.tsv

   • config/units.tsv

   • fastq files

   • adapter trimming

   • stradedness

4. run workflow

snakemake --cores all --use-conda

5. generate report

snakemake --report report.zip