Lecture notes

This page contains all the slides that I taught.

TIGP Introduction to NGS

  1. Introductory lecture [v2018] Download
  2. Introduction II Linux, R, and other-Tools [v2018] Download
  3. Genome Assembly and case studies [v2018] Download
  4. Read Mappings [v2018] Download
  5. From Alignment to phylogenetic tree (Jiang Ming Chang) [v2018] Download
  6. DNA/RNA preparation and different sequencing technologies (Meiyeh Lu) Download
  7. RNAseq and Genome annotation [v2018] Download
  8. Comparative Genomics [v2018] Download
  9. Population Genomics (John Wang)
  10. Amplicon / Metagenomics [v2018] Download
  11. Practical one: Linux and R
  12. Practical two: RNAseq mapping and EdgeR
  13. Discussion
  14. Final Report

Example Dataset

  1. myoviridae_healthy.txt (taken from R into with GGPLOT).
  2. worms.txt (Example taken from R exercises and examples).
  3. Survey2.csv (questionnaire survey).
  4. R examples in Lecture 2.

TIGP B2

  1. NGS Analytics [v2019] Download
  2. Comparative Genomics Download

TIGP Microbial Diversity and Ecology

  1. Fungal Diversity [v2019] Download

GSB 2018

  1. Comparative Genomics Download
  2. Introduction to Transcriptome Download

Homework: Choose a paper that combines both comparative genomics and RNAseq to address a biological question. The paper has to be published from 2015-2018. Please write a review, be critique on the techniques used and assess the strength and weaknesses of the paper. Please hand in before 12/29 (one month’s time to write the homework). Late or no hand in of your work will be marked 0.

長庚 2019

  1. NGS 次世代定序 Introduction Download

Note

Email ijtsai at sinica.edu.tw if you have any problems/suggestions/want to use the slides