pipeline-rnaseq

Pipeline for analyzing in-vitro RNA-Seq experiments.

Cloning the repo

This pipeline using Git submodules. The easiest way to clone this repo (with a recent version of git) is

git clone --recurse-submodules https://github.com/pvstodghill/pipeline-rnaseq.git

Installing prereqs

One of the following:

• Conda

You will also need,

• Snakemake
• Perl
• Perl's YAML module

Configuring the pipeline

Create the configuration files

For the example data,

1. Copy example/config.yaml to config.yaml.

To run the pipeline on your own data,

1. Copy config.template.yaml to config.yaml. Edit config.yaml according to your needs and local environment.

Running the pipeline

To run the pipeline using local copies of the software components:

snakemake

To run the pipeline using Conda to provide software components:

snakemake --use-conda

To run the pipeline using Mamba to provide software components:

snakemake --use-conda --conda-frontend mamba

Software components

The following software is used by this pipeline,

• Bowtie2
• DESeq2
• Falco
• Fastp
• featureCount from Subread
• R
• Samtools