Lecture notes¶
This page contains all the slides that I taught.
GSB 2022 R practicals¶
TIGP Introduction to Genomics / (NGS)¶
- Introductory lecture [v2020]
Download - Introduction II Linux, R, and other-Tools [v2020]
Download - Read Mappings [v2020]
Download - Genome Assembly and case studies [v2020]
Download - Comparative Genomics [v2020]
Download - RNAseq and Genome annotation [v2020]
Download - From Alignment to phylogenetic tree (Jiang Ming Chang) [v2020]
Download - Population Genomics (John Wang) [v2020]
Download - Amplicon / Metagenomics [v2020]
Download - Study week (no class)
- DNA/RNA preparation and different sequencing technologies (Meiyeh Lu) [v2020]
Download - Midterm Exam (27t May)
- Final presentation I (Students)
- Final presentation II (Students)
- R tutorial I [v2020] ; Attendance optional ;
Download - Practical two: RNAseq mapping and DEseq2 (not updated yet) ; Attendance optional
- no class
First assignment (dealine 25th March): Find a paper that has a combination of comparative, population, RNAseq or metagenomics in your field (at least 2). Write a protocol on how the bioinformatics part of the study was conducted (what tools, what version, input, output). As detailed as possible.
- Second assignment (deadline 15th April):
- Construct a BWT of the following sequence ANNABANANA . Show your working.
- What is the output of last column?
- Write out how you searched the string ANNA
- Final presentation.
- Each of you will present a 10 minute talk about your “genomic projec proposal”, followed by 5 minutes of questions. This can be resequencing, de novo assembly, RNAseq, amplicons, metagenomics, anything as long as it involves sequencing. This can not be your current work, so you need to think outside the box. The only required format is your first slide -> briefly introduce yourself and what you are currently working on. The second slide is the start of proposal with a title of your project. Any number of slides are fine as long as you can keep track of time. Order of students will be chosen randomly. Marks will be normalised by week, for example the marks of first group will be normalised based on the performance of presenters in week 14.
- Midterm exam: Self explanatory. Two hours.
- All the guest speakers’ lectures won’t be tested.
Final marks submitted
Example Dataset (v2018 ; not updated yet)¶
myoviridae_healthy.txt(taken from R into with GGPLOT).worms.txt(Example taken from R exercises and examples).Survey2.csv(questionnaire survey).R examples in Lecture 2.
TIGP B2¶
- Comparative and Evolutionary Genomics [v2022]
Download - Genome assemblies and case studies [v2022]
Download
Assignment (take home question): First choose a group of species, or a species. Then please write a short review (~10 references) on how analyses of comparative/population genomics have been transformed by recent advances (algorithm and experimental approaches) in sequencing.