​​​​Module-2.jpg

NOTE:  
_______

  • Cost also includes access to computer during training & Tea/coffee and a light lunch ​but excludes transport and accommodation.

  • Proof of payment or commitment to pay
    ​(i.e., Purchase Order) must be provided before date of training.


Course O​utline


  04 - 06 JULY​ 2022
Genome-wide SNP data analysis: Basic population genetic analysis

________________________________________________________________________________________________________ 
Course will run from 09h00 - 16h00 everyday

​Facilitators:  
Dr Khanyisile Hadebe (Coordinator; Senior Researcher: Animal Genomics)
Dr Magriet van Der Nest (Senior Researcher: Bioinformatics)​

Module content:

Day ​Content​SoftwareFacilitator
​1

Introduction to array-based Genome-wide SNP genotyping:

  • Quality control
  • ​Data file management​

PLINK​
VCFTo​ols
FCGene
BEAGLE
Fastphase

Khanyisile Hadebe,

Magriet Van der Nest

​2

~ Introduction to R

~ Population analysis

PLINK
ADMIXTURE
R/RStudio

Khanyisile Hadebe

Magriet Van der Nest

​3

​​Runs of Homozygosity (ROH)

​Copy Number Variant (CNVs)

R/RStudio

Khanyisile Hadebe

Magriet Van der Nest

​4

Hands on data analysis 

The trainee can bring their own data to analyse or use the dummy data provided.

Khanyisile Hadebe

Magriet Van der Nest​


For enquiries on the programme, registration and payment details, 
email Dr Adeola Rotimi at RotimiA@arc.agric.za


~~~ Back to Genomics Training Programmes ~~~

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