Mar 20-21, 2018
9:00 am - 5:00 pm on Mar 20, 9:00 am - 12:00 pm on Mar 21
Instructors: Sue McClatchy, Dan Gatti
Helpers: Yuka Takemon
Where: Bioinformatics Training Room 1540, 600 Main Street, Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps. JAX employees can locate the bioinformatics training room in building 1, unit 5 on this campus map.
When: Mar 20-21, 2018. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email susan.mcclatchy@jax.org for more information.
SCHEDULE
| 09:00 | Introduction |
| 09:15 | Input File Format |
| 09:30 | Calculating Genotype Probabilities |
| 10:00 | Calculating A Kinship Matrix |
| 10:45 | Coffee |
| 11:00 | Special covariates for the X chromosome |
| 11:15 | Performing a genome scan |
| 12:00 | Lunch break |
| 13:00 | Finding LOD peaks |
| 13:30 | Performing a genome scan with a linear mixed model |
| 14:00 | Performing a genome scan with binary traits |
| 14:30 | Coffee |
| 14:45 | Performing a permutation test |
| 15:30 | Estimated QTL effects |
| 16:00 | SNP association |
| 16:45 | Wrap-up |
| 09:00 | QTL analysis in Diversity Outbred Mice |
| 10:45 | Coffee |
| 11:00 | QTL analysis in Diversity Outbred Mice (continued) |
| 11:45 | Wrap-up |
| 12:00 | End |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.