BeBoL workshop: Genotyping-by-Sequencing, Genome-wide association study and Genomic Prediction.
Date: 15-17 September 2015, Brussels.
Venue: Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium.
Expected backgorund of the participant: basic knowledge of R, and some familiarity with NGS data. Familiarity with basic Linux commands is helpful, but not required.
Registration: free but mandatory. The workshop is limited to 25 participants.
Instructors:
- Dr. Jeff GLAUBITZ, Buckler Lab for Maize Genetics and Diversity, Cornell University (http://www.maizegenetics.net/#!jeff-glaubitz/cxmy)
- Dr. Peter James BRADBURY, Buckler Lab for Maize Genetics and Diversity, Cornell University (http://www.maizegenetics.net/#!peter-bradbury/c16k4)
- Dr. Deniz AKDEMIR, Cornell Center for Comparative and Population Genomics, Cornell University (http://vivo.cornell.edu/display/da346)
Program at a glance (see below for the detailed program):
- 15 Sept. 2015: Genotype-by-sequencing (GBS) using the TASSEL software
- 16 Sept. 2015: Genome-wide association study (GWAS)
- 17 Sept. 2015: Genome-wide prediction of quantitative Traits
This workshop is organized and supported by the Belgian Network for DNA Barcoding, BeBoL (FWO).
Full program:
TASSEL 5 Overview (Tues Sept 15 – Jeff, Peter – 50 min AM)
- What TASSEL does
- Graphical vs. Command Line Interface
- Resources for TASSEL Users: Tassel web pages; Tassel Google Group
- Obtaining, Installing, Updating TASSEL 5
TASSEL-GBS (Tues Sept 15)
- GBS assay background (Jeff – 50 min AM)
- GBSv2 pipeline explanation (Jeff – 50 min AM)
- Hands on GBSv2 Exercise (Jeff – 50 min PM)
- Filtering GBS SNPs and Taxa (Jeff – 20 min PM)
- Imputing GBS SNPs (Peter – 90 min PM): FSFHapMap; FILLIN; LD KNNi; Projection of high density, whole genome SNPs; Beagle and other software.
Analysis of Genotypes (Wed Sept 16 – Jeff, Peter – 50 min AM)
- Geno Summary
- Diversity & LD
- Distance Matrix & Cladogram
- Kinship & PCA
GWAS & genome-wide prediction of quantitative Traits (Wed Sept 16 – Peter – 120 min AM)
- GLM
- MLM
- Stepwise
- Fast Association for eQTL data
- Genome selection (GS) or genome-wide prediction of quantitative Traits
The Big Picture (Wed Sept 16 – Peter, Jeff – 50 min PM)
- Limitations of TASSEL
- Applications/use cases of TASSEL/GBS/GWAS/GS
- Experimental Design considerations for GBS/GWAS/GS studies
Resources for prospective TASSEL programmers (Wed Sept 16 – Jeff – 20 min PM)
- TASSEL Hackathon
- How can I obtain/modify/contribute to the TASSEL Source code?
Genome-wide prediction of quantitative Traits (Thurs Sept 17 – Deniz)
- What is Genomic Prediction (aka Genomic Selection)? (20 mins)
- Few basics (R, data preparation). (30 mins)
- One step vs Two Steps Approaches to GP (2 hours):
- Two-step analysis (1 hours): rrBLUP; LASSO; BayesB; GBLUP; RKHS
- One-step analysis (1 hours): rrBLUP; BayesB; GBLUP; RKHS
- Factors Affecting the Success of GP (20 mins)
- Balancing Genetic Gains and Diversity (30 mins)
- Selection Indices (20 mins)
- Exercises (1-2 hours)