CEPLAS RNASeq Workshop 2022
This ARC provides all course material required for the CEPLAS RNASeq Workshop (August 22 - 24, 2022). Please explore the Reader for details.
ARC disclaimer
Please note, that this workshop repository does not take advantage of all ARC features, which would simply be out of scope for a three day workshop focusing on RNA-Seq data analysis. If you want to learn more about ARCs and related DataPLANT tools and services, please visit the DataPLANT website.
The basic ARC structure summarized
| directory | content |
|---|---|
| studies | external data and sample metadata |
| assays | measurement data (i.e. "raw" sequence data) and metadata |
| workflows | computational analyses (i.e. "scripts") |
| runs | outputs of workflow |
Material added to the ARC for this workshop
| directory | content |
|---|---|
| _reader | The basis to this reader (written in LaTeX) |
| _slides | Slides presented during the workshop |
| _handouts | Cheat sheets and additional materials |
| runs/_backups | Backups for runs, in case a workflow unexpectedly did not work or takes too long |
Docker
In order to use the tools and run all scripts mentioned in the reader, you need to install some dependencies on your machine. This is done using the docker images available at sciebo or built from scratch.
Ready to use docker images
...can be downloaded from sciebo
- https://uni-duesseldorf.sciebo.de/s/53pA9W9TbOKTgGQ
- See reader section 4.3 for details
- Password provided via email or during class
Build docker image
If you want to build the docker images from scratch (rather than downloading from sciebo), follow the respective instructions in
Take home
Find three options for using the images from the course on your own computer in TakeHome.md.