TREND course at Khartoum university

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13th-17th March, proposed schedule:

Day 1

• Introduction to NGS analysis methods
• Introduction to R and Unix
• Practical: Unix
• Practical: R

  Day 2

• Graphics in R
• Alignment basics and RNAseq
• Practical: Graphics in R
• Practical: alignment basics and RNAseq

  Day 3

• Approaches to sequence mapping and genotyping
• Approaches to transcriptome analysis
• Practical: RNAseq QC and differential expression analysis
• Practical: RNAseq visualisation, discovering novel isoforms, visualise and summarize the output

  Day 4

• Aligning of exome sequences to the human reference and variant calling
• Target gene identification
• Practical: Whole exome data and variant calling
• Practical: Target gene identification

  Day 5

• WES case study: Aligning of exome sequences to the human reference
• WES case study: Target gene identification
• RNASeq case study: RNAseq QC and differential expression analysis
• RNASeq case study: RNAseq visualisation, discovering novel isoforms, visualise and summarize the output

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Things to do in advance

• [x] write the materials (make this a separate sprint issue)
• [x] get yellow fever vaccination (see http://www.who.int/ith/ITH_Annex_I.pdf?ua=1)
• [x] book flights
• [x] get visa https://www.gov.uk/foreign-travel-advice/sudan/entry-requirements
• [x] most likely need to transit through Egypt, if so organise transit visa https://www.gov.uk/foreign-travel-advice/egypt/entry-requirements
• [x] make sure all materials credit Trend and H3ABioNet http://h3abionet.org/ and MSL