Curso

Review and implementation of bioinformatics tools and techniques for breeding and management of Argentinian sheep

El presente curso se dictará en el marco del Proyecto de FAO/IAEA TCP RLA/5/071 (ARCAL CXLIV) “Decrease in the rate of parasitosis in sheep”.

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Unidades
Enfoque:
Científico
Disertante/s: Mario Andres POLI, Mario BARBATO
Fecha:
De Lunes, 11 Noviembre, 2019 - 09:00 hasta Viernes, 15 Noviembre, 2019 - 16:30
Lugar:
Contactos INTA:
Correo electrónico:
raschia.maria@inta.gob.ar
El INTA es Organizador
Destinado a:
Profesionales

 Working Agenda and timetable 

 

Day

Event:   Lecture and practice

Facilitator

Monday November 11th, 2019

 

9.00 – 9.15

 

9.15 – 10.15

 

10.15 – 10.45

10.45 – 12.00

Welcome address and presentation of IAEA-ARCAL project.

Preparation of phenotype and covariate data files for association studies.

Coffee break

Manipulation of whole-genomic sequence data.

Association analysis on candidate-genes. Assessment of relevant effects to consider in models used for association analysis.

Poli, Mario

 

Barbato, Mario

 

 

Barbato, Mario

 

 

 

 

12.00 – 13.30

Lunch break

 

 

13.30 – 16.30

Review the existing bioinformatics facility. Introduction and implementation of bioinformatics pipelines for data quality control and downstream analysis.

 

Barbato, Mario & Animal Molecular Markers Research Staff

Tuesday  November 12th, 2019

 

8.45 – 10.00

 

10.00 – 10.30

10.30 – 12.00

Genome-wide association analysis on continuous data from related animals with pedigree information.

Coffee break

Introduction to R scripts for visualization of QC and GWAS results.

Barbato, Mario

 

 

Barbato, Mario

 

12.00 – 13.30

Lunch break

 

 

13.30 – 16.30

Review of preliminary results obtained from association analyses at genome-wide level and on candidate genes. Discussion and interpretation of results.

Barbato, Mario &  Animal Molecular Markers Research Staff

Wednesday   November 13th, 2019

 

8.45 – 10.00

10.00 – 10.30

10.30 – 12.00

General considerations on imputation.

Coffee break

Imputation of genotypes on related animals using low and medium density SNP microarrays. Reference population.

Barbato, Mario

Barbato, Mario

 

12.00 – 13.30

Lunch break

 

 

13.30 – 16.30

Linkage disequilibrium decay analysis.  

Barbato, Mario

Thursday  November 14th, 2019

 

8.45 – 10.00

10.00 – 10.30

10.30 – 12.00

Extracting basic diversity measures.

Coffee break

Estimating Reynold’s distance and drawing Neighbornet tree.

Barbato, Mario

 

Barbato, Mario

 

 

 

12.00 – 13.30

Lunch break

 

 

13.30 – 16.30

Population structure and admixture analysis.

Barbato, Mario

Friday  November 15th, 2019

 

8.45 – 10.00

 

10.00 – 10.30

10.30 – 12.00

Estimation of Nicholson FST and identifying outlier SNP loci to detect selection signatures.

Coffee break

Estimation of Nicholson FST and identifying outlier SNP loci to detect selection signatures (contd).

Barbato, Mario

 

 

Barbato, Mario

 

12.00 – 13.30

Lunch break

 

 

13.30 – 16.30

Closing remarks.