Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Introduction	What are expression quantitative trait loci (eQTL)? How are eQTL used in genetic studies?
Duration: 00h 12m	2. Genetic Drivers of Pancreatic Islet Function	What is the hypothesis of an example eQTL study?
Duration: 00h 42m	3. Load and explore the data	What data are required for eqtl mapping?
Duration: 01h 27m	4. Review Mapping Steps	What are the steps involved in running QTL mapping in Diversity Outbred mice?
Duration: 02h 27m	5. Mapping A Single Gene Expression Trait	How do I map one gene expression trait?
Duration: 03h 27m	6. Mapping Many Gene Expression Traits	How do I map many genes?
Duration: 04h 27m	7. Creating A Transcriptome Map	How do I create and interpret a transcriptome map?
Duration: 05h 27m	8. Transcriptome Map of cis and trans eQTL	How do I create a full transcriptome map?
Duration: 05h 57m	9. Maximum eQTL Peaks and Nearby Genes	How do I display maximum eQTL peaks and nearby genes?
Duration: 06h 27m	10. Interpreting qtl2 results	How do I interpret qtl2 results?
Duration: 06h 57m	11. Mediation Analysis	What is mediation analysis? How do I explore causal relations with mediation analysis?
Duration: 07h 27m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Data Sets

---

Download the data zip file and unzip it to your Desktop

Software Setup

---

Install Gcloud tools.

Open a Google Cloud SDK Shell window and run the following command:

gcloud compute ssh --zone "us-east1-b" "sumnergcp-controller" --tunnel-through-iap --project "jax-presgraves-edusumner2"

This will open another terminal window which will connect to the Google Cloud Platform (GCP).

GCP window with slurm prompt

Next, type the following command:

module load rstudio

This will produce the following message:

Rstudio 4.4.1 loaded. Use the command 'sbatch -w sumnergcp-computenodeset-1
rstudio-session.job' to start a new session on node 2. You can change the node
number if you want to run on a different node. The cluster has 30 compute nodes
ranging from 0 to 29

Follow the instructions in the message by typing the following command into the GCP window.

sbatch -w sumnergcp-computenodeset-1 rstudio-session.job

This will start a compute queue job which will be reported as:

Submitted batch job <N>

where is an integer that is your slurm job ID. The login node is spawning a compute node where RStudio will run.

After about two minutes, you should see a file like this in your home directory:

rstudio-server.job.<N>

where is the same integer as your batch job ID.

View the contents of the file using teh cat command:

cat rstudio-server.job.<N>

You will be instructions which tell you how to access your GCP RStudio instance along with a user name and password.

> cat rstudio-server.job.53
**********************************************************************
  RStudio server IP address: 35.196.22.80
  The name of the compute instance running the server is sumnergcp-computenodeset-1
***********************************************************************

Follow the instaructions below to connect to your
rstudio instance:

1. point your web browser to http://35.196.22.80:8787
2. log in to RStudio Server using the following credentials:

  user: dan_gatti_jax_org
  password: Dw7Qr3ejbOwBmtOPHxQt

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f 53

Install R packages:

{r eval=FALSE} install.packages(c('BiocManager', 'remotes', 'tidyverse', 'qtl2'))

remotes::install_github('churchill-lab/intermediate')

Details

Setup for different systems can be presented in dropdown menus via a spoiler tag. They will join to this discussion block, so you can give a general overview of the software used in this lesson here and fill out the individual operating systems (and potentially add more, e.g. online setup) in the solutions blocks.

Windows

Use PuTTY

MacOS

Use Terminal.app

Linux

Use Terminal