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
- chef-rebar3
-erlang
Recipes
rna-seq::bowtie
installs Bowtie 1.1.2 which is a Bowtie release old enough to be compatible with TopHatrna-seq::data
downloads the Drosophila melanogaster reference genome from iGenomes and the simulated transcripome samples for two conditions from NCBIrna-seq::tools
installs SAMtools, Cufflinks, R, CummeRbund, and triggers the recipes for Bowtie and TopHatrna-seq::tophat
installs TopHat 2.1.1 which is the last TopHat release published before the tool was discontinued in 2016rna-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