sangerpathogens/rnaseq repository overview

⁠rnaseq

A RNA seq pipeline for the Pathogen and Microbes research group at the Wellcome Sanger Institute

⁠Contents (edit as fit)

• Introduction⁠
• Installation⁠
  • Pip⁠
  • Docker⁠
• Usage⁠
• License⁠
• Feedback/Issues⁠

⁠Introduction

RNA-Seq Expression Analysis: Calculates rna-seq expression (Reads Mapped and RPKM) based on selected protocol:

• Standard
• dUTP
• Croucher For more information on this pipeline see Pathogen Informatics RNA-Seq Expression Pipeline.

⁠Installation

⁠Pip

Install master:

pip install git+https://github.com/sanger-pathogens/rnaseq.git

Install a specific version:pip install git+https://github.com/sanger-pathogens/rnaseq.git@<TAG>. Example:

pip install git+https://github.com/sanger-pathogens/[email protected]

Once install, rnaseq can be run directly:

rnaseq.py -h

⁠Docker

Pull the latest image:

docker pull sangerpathogens/rnaseq:latest

Run in a container:

docker run --rm -it -v /home:/home sangerpathogens/rnaseq:latest rnaseq.py -h

To pull and run a specific version, just replace latest by the version number. Example:

docker pull sangerpathogens/rnaseq:0.0.1
docker run --rm -it -v /home:/home sangerpathogens/rnaseq:0.0.1 rnaseq.py -h

⁠Usage

Please run rnaseq.py -h for help

⁠License

rnaseq is free software, licensed under GPLv3⁠.

⁠Feedback/Issues

Please report any issues to the issues page⁠ or email [email protected]⁠.