README.md

Working with Protozoan Parasite Database Resources 2022 (Africa)

Learn how to use online resources for genomic-scale data analysis of protozoan parasites

Course Overview

Course website

Instructors and Speakers

• Vincent Appiah - University of Ghana, Ghana

• Luisa Berná - Institut Pasteur de Montevideo, Uruguay

• Ulrike Böhme - University of Liverpool, UK

• Omar Harb - University of Pennsylvania, USA

• Collins Misita - University of Ghana, Ghana

• Rowland Osii - University of Glasgow, UK

• Thomas Otto - University of Glasgow, UK

• Dinkorma Ouologuem Toure - Université des Science, Techniques et des Technologies de Bamako, Mali

Course Manual

Day 1:

• Basic searches in VEuPathDB:

  • Basic searches in VEuPathDB – Site search

  • Basic searches in VEuPathDB – Search strategies

  • Basic searches in VEuPathDB – Organism Preferences (optional exercise)

• The gene page in VEuPathDB

• Introduction to Artemis

• Genome Browser Basics

• Group exercise: Interpreting RNAseq data in the genome browser/Apollo

• Group exercise: Genome annotation with Companion

Day 2:

• Group exercise: Companion results analysis

• Companion results analysis. Comparative Genomics

• Introduction to Linux

• Introduction to HTS & mapping

• Variation searches in VEuPathDB: SNPs & CNVs

Day 3:

• Intro to RNA Seq Analysis - will be a talk - slides will come.

• Group exercise: Starting and RNA Seq analysis workflow in Galaxy

  • Groups
  • RNA Seq in Galaxy part 1

• Transcriptomics/proteomic searches in VEuPathDB

• Orthology

Day 4:

• Exploring RNA Seq results from Galaxy part 2, including analysis of results in VEuPathDB

• Host response

Day 5:

• Group projects