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General Information

This course introduces genetic mapping using qtl2, a R package for analyzing quantitative phenotypes and genetic data from complex crosses like the Diversity Outbred (DO). Genetic mapping with qtl2 allows researchers in fields as diverse as medicine, evolution, and agriculture to identify specific chromosomal regions that contribute to variation in phenotypes (quantitative trait loci or QTL). The goal is to identify the action, interaction, number, and precise location of these regions. The course concludes with a complete analytical workflow from a study of DO mice.The lesson is adapted from Karl Broman's software, tutorials, and book co-authored with Saunak Sen, A Guide to QTL Mapping with R/qtl.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Dec 11th, 14th, 16th, and 18th, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email facilitator@datascience.wisc.edu for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to researchers who want to employ genetic mapping to identify, quantify, and characterize quantitative trait loci.

Prerequisite: Some R programming skills are required for successful participation. If you can manipulate R data structures (e.g. lists, matrices, data frames) you are ready for this course.

Code of Conduct

Everyone who participates is required to conform to the Code of Conduct.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

All times are Central Standard Time (CST). Add one hour for Eastern Standard Time (EST).

Setup

To participate in a workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

• Two monitors: If you have two monitors, plan to have your terminal up on one monitor and the video conferencing software on the other.
• Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
• Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

qtl2

The qtl2 package contains code for haplotype reconstruction, QTL mapping and plotting.

Option 1: R/qtl2 is not yet available on CRAN, but it can be installed from a mini-CRAN at rqtl.org. Make sure you have the latest version of R (3.4.4).

Option 2: Alternatively, you can install R/qtl2 from its source on GitHub. (But note that compiling the C++ code can be rather slow.)

On Windows, you’ll need Rtools.

On Mac OS X, you’ll need the command-line developer tools, as well as gfortran.

You then need to install the devtools package, plus a set of package dependencies: yaml, jsonlite, data.table, and RcppEigen. (Additional, secondary dependencies will also be installed.) Start RStudio, then copy and paste the following code into the R console in RStudio.

install.packages(c("devtools", "yaml", "jsonlite", "data.table", "RcppEigen", "RSQLite", "qtl"))

Finally, install R/qtl2 using devtools::install_github(). Copy and paste the following code into the R console in RStudio.

library(devtools)
install_github("rqtl/qtl2")

Data files and project organization

1. Make a new folder in your Desktop called mapping. Move into this new folder.

2. Create a data folder to hold the data, a scripts folder to house your scripts, and a results folder to hold results.

Alternatively, you can use the R console to run the following commands for steps 1 and 2.

setwd("~/Desktop")
dir.create("./mapping")
setwd("~/Desktop/mapping")
dir.create("./data")
dir.create("./scripts")
dir.create("./results")

1. Please download the following large files before the workshop, and place them in your data folder. You can download the files from the URLs below and move the files the same way that you would for downloading and moving any other kind of data.

• cc_variants.sqlite doi:10.6084/m9.figshare.5280229.v2, variants in the Collaborative Cross founders (3 GB)
• mouse_genes.sqlite doi:10.6084/m9.figshare.5280238.v4 full set of mouse gene annotations (677 MB)
• mouse_genes_mgi.sqlite doi:10.6084/m9.figshare.5286019.v5 just the MGI mouse gene annotations (11 MB)
• DO QTL data Dan’s DO data from the benzene study

Alternatively, you can copy and paste the following into the R console to download the data.

setwd("~/Desktop/mapping")
download.file("https://ndownloader.figshare.com/files/9746485", "./data/cc_variants.sqlite")
download.file("https://ndownloader.figshare.com/files/9746458", "./data/mouse_genes.sqlite")
download.file("https://ndownloader.figshare.com/files/9746452", "./data/mouse_genes_mgi.sqlite")
download.file("ftp://ftp.jax.org/dgatti/qtl2_workshop/qtl2_demo.Rdata", "./data/qtl2_demo.Rdata")

You will need these for the final lesson episodes on SNP association mapping and QTL analysis in Diversity Outbred mice.