ASHG 2019 workshop:
RNA-seq for Mendelian disease diagnostics

A hands-on tutorial through bioinformatic tools and workflows

Link to the workshop presentation: https://tinyurl.com/RNA-ASHG-presentation

Link to the tutorial (colab notebook): http://tinyurl.com/RNA-ASHG-colab

Welcome to the ASHG RNA-seq workshop!

We set up a Slack workspace to facilitate communication among the participants as well as the rare disease RNA-seq community in general. Please sign up here. We hope to have active conversations and interactions during the workshop and also in the future within this workspace.

During the workshop we will use an interactive R notebook (IR notebooks), which is similar to the well-known IPython notebook. After each section there will be a little exercise that you can do to test your new skills.

This workshop is accompanied with a colab notebook. In order to edit it, please save a copy of the notebook to your private Google Drive account.

How to make the most out of this tutorial

To use this tutorial most efficiently, you should follow some rules:

1. Login to your Google account or create one. This is needed to run Colab.
2. Open the notebook
3. Save a copy in your personal Google Drive (click on File -> Save a copy in Drive ...)
4. Make sure to execute the first code cell which contains the r-env-setup-script.R command. This is needed to setup the R environment (takes ~3 minutes).
5. Have fun learning new skills!
6. Communicate with your peers in person (most important) or on Slack!
7. Ask for help on Slack if needed

If you run into any problems, feel free to check out our FAQ. If you are new to programming in R or to notebooks in general have a look into the getting started guide.

Relevant presentations during ASHG2019

Please post any relevant sessions, presentations, and posters on Slack (channel #posters-at-ashg) or do a PR.

• Session E #63: RNAseq to Augment Variant Interpretation and Disease Diagnosis
• Session #112: Exome and RNA-based Sequencing Methods for Variant Interpretation to Improve Clinical Utility
• FraseR: A statistical method to detect aberrant splicing events in RNA-seq data