RNA-seq

This workflow exemplifies the comparison of DNA expression levels in two experimental conditions from RNA-Seq data. It reimplements a study by Trapnell et al. 2012.

A detailed description can be found on the Cuneiform website. This cookbook installs all necessary tools, downloads all necessary data, sets up Cuneiform, and places the workflow in a predetermined location. The cookbook can be run on any system in a virtual machine. For running the cookbook natively, an Ubuntu 16.04 or higher is required.

Below you find installation instructions for, both, the native and the virtual machine setup.

Requirements

Platforms

• Ubuntu 18.04

Cookbooks

• chef-cuneiform
  • chef-rebar3 -erlang
    • build-essential
    • mingw
    • seven_zip
    • windows
    • yum-epel
    • yum-erlang_solutions

Recipes

• rna-seq::bowtie installs Bowtie 1.1.2 which is a Bowtie release old enough to be compatible with TopHat
• rna-seq::data downloads the Drosophila melanogaster reference genome from iGenomes and the simulated transcripome samples for two conditions from NCBI
• rna-seq::tools installs SAMtools, Cufflinks, R, CummeRbund, and triggers the recipes for Bowtie and TopHat
• rna-seq::tophat installs TopHat 2.1.1 which is the last TopHat release published before the tool was discontinued in 2016
• rna-seq::workflow installs the RNA-seq Cuneiform workflow under /opt/wf

Running the Workflow

If you set up the workflow via kitchen converge, log into the machine by typing

kitchen login

Execute the workflow script by entering

cuneiform -d /opt/data /opt/wf/rna-seq.cfl

Authors

• Jörgen Brandt (@joergen7) joergen@cuneiform-lang.org

License

Apache 2.0