RNA-seq Analysis

A Snakemake 🐍 pipeline to analyze RNA-seq expression data.

Author: Kristina Sungeun Song

Installing Snakemake

Please follow the instructions to install the Snakemake workflow management tool. We recommend using Conda/Mamba to install Snakemake.

This Snakemake workflow has been tested with v7.32.4.

Running the Snakemake workflow

For a dry-run of this Snakemake workflow, simply run the following code from RNAseq/.

snakemake -n

To run this Snakemake workflow, simply run the following code from RNAseq/.

snakemake --profile profile_slurm

OR

snakemake --profile profile_local

Steps

1. Trimming: Trimmomatic
2. Read mapping: Kallisto, STAR
3. Read quality check: FastQC, Picard, PCA, MultiQC
4. Differential expression analysis: DESeq2
5. Alternative splicing analysis: rMATS (paired & non-paired)