Lecture slides

Unix / R pre-course

• Aug 22: Slides from Pre-course

Fundamentals of Molecular biology

• Sep 4 : Slides from Molecular Biology

High throughput sequencing (HTS)

• Sep 4 : Slides from HTS
• Sep 5 : Slides from HTS - library prep
• Sep 5 : Slides from HTS - PacBio
• Sep 5 : Slides from HTS - Basic file formats
• Sep 6 : Slides from HTS - Data pre-processing
  • Script - HTS

Algorithms

• Sep 6 : Slides from HTS - Algorithms alignment
• Sep 11 : Slides from HTS - Algorithms mapping
  • Sep 11 : Exercise from HTS - Algorithms mapping
  • Sep 11 : Exercise Answers from HTS - Algorithms mapping

De novo genome assembly

• Sep 11 : Slides and practicals from genome assembly
• Sep 11 : Link to Etherpad

RNA-seq analysis

• Sep 18 : Slides from RNA-seq - Introduction
• Sep 18 : Slides from RNA-seq - Transcriptome
• Sep 19 : Slides from RNA-seq - Experimental design
• Sep 19 : Slides from RNA-seq - Differential expression
• Sep 20 : Slides from RNA-seq - After DE
• Sep 18-20 : Slides from RNA-seq - Case study (Updated)
  • Script - RNASeq
  • Script - CummeRbund
  • Script - DESeq2

Variant calling

• Sep 25 : Slides from VC - slide deck 1
• Sep 25 : Slides from VC - slide deck 2
• Sep 26 : Slides from VC - slide deck 3
• Sep 27 : Slides from VC - slide deck 4
• Sep 27 : Bayesian statistic example
• Sep 27 : Slides from VC - slide deck 5
• Sep 27 : Slides from VC - slide deck 6

Statistical genomics

• Oct 09 : Slides from Statistical genomics - part 1
• Oct 09 : Slides from Statistical genomics - complete