Diversity Outbred (DO) bulk RNA-Seq pipeline

Getting started

Clone this repository in your computing environment

#!/usr/bin/bash
# make sure git is set up to handle SSH login
git clone git@github.com:Farber-Lab/Diversity_outbred_bulk_RNA-Seq.git
cd Diversity_outbred_bulk_RNA-Seq/

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Note: GitHub no longer supports password authentication on https:// URLs. SSH login methods are preferred. To setup SSH based login please follow this documentation. Alternatively, a token can be used for authentication. Use GitHub settings to generate a token.

Core Dependencies

The following dependencies should be installed in the computing environment and available in the $PATH

Genomics utilities

• fastqc/0.11.5
• multiqc/1.11
• trimmomatic/0.39
• hisat2/2.1.0
• Samtools/1.12
• stringtie/2.1.0
• peer/1.3

Language interpreters

• python/2.7.16
• python/3.8.8
• R/4.2.1

Documentation

• Modules used in this workflow
• Notes for Rivanna Users (UVA internal)