/Diversity_outbred_bulk_RNA-Seq

A repository for DO bulk RNA-Seq data analysis

Primary LanguagePythonMIT LicenseMIT

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/

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