In this module, we will cover basic analysis methods for Genome-wide Association Analysis.
Overview of GWAS, principles behind GWAS, and using SNP genotyping data for GWAS
Interpreting GWAS results, and introduction to post-GWAS data analysis
Introduction to internship special problems
Hands-on exercises and wrap-up
Learning contents (all at Module 3 google drive)
Day 11 (July 18)
Materials for today (gdrive)
Foundations of GWAS (pdf), analysis using TASSEL (pdf)
Today's recap
Zoom video
Zoom chat
Evaluation form
Day 12 (July 19)
Continuation: GWAS analysis using TASSEL (phenolics data)
GWAS peak determination and LD clumping (pdf)
Population structure and multiple testing issues (pdf)
Exploring other GWAS models (pdf)
Using SNP-Seek data for GWAS analysis (pdf)
Advanced GWAS
GWAS Peak haplotype analysis (pdf)
Overview of mixed linear models (pdf)
Today's recap
Zoom video
Evaluation form
Day 13 (July 20)
Materials for today (gdrive)
Asynchronous day!!!
Day 14 (July 21)
Interns: Please do the following first:
Accomplish evaluation forms
Fill out Rock poll
Send your questions for clarification/further explanation to Rock space or directly to resource person in Rock
Open Q&A / tutorials catch-up
SNP calling and associated processes... [CHEAT SHEET]
shell history (doc) ,using Palay 5-6 sample read pair
GWAS more tutorials (materials at gdrive)
GWAS instructions (doc)
shell history for tutorial (doc)
dataset used in tutorial- another trait , NOT the phenolic one!
Today's recap
Zoom video , chat
Evaluation form
Day 15 (July 22)
Materials for today
phenotype files (your assigned trait!)
Continue working on assigned phenotype trait (special project for 6 week internship)
Supplemental Resources: GWAS tutorials
Marees et al., NCBI
Breheny et al. at github
Uffelmann et al., Nature reviews