Program 2021
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Lectures and exercises will take place on Discord (https://discord.gg/JxV3pHyHgV). Please register with your full name. Will use Discord for online classes and collaboration with your project partners.
The course has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Friday 22th of January.
This term, we will be using Piazza for class discussion. The system is highly catered to getting you help fast and efficiently from classmates, the TA, and myself. Rather than emailing questions to the teaching staff, I encourage you to post your questions on Piazza here
Course Program - January 2021
Monday, January 4
Introduction - Next Generation Sequencing
- 9:00am-9:30am
- Introduction to course & Pre-test (Lecture slides) (Pre-test)
- Gabriel Renaud
- 9:30am-10:00am
- Introduction to NGS (Lecture slides)
- Gabriel Renaud
- 10:00am-10:45am
- 2nd and 3rd generation NGS Technologies (Lecture slides)
- Gabriel Renaud
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Tech talk group formation and group work (Lecture slides) (Student Groups 2021)
- Gabriel Renaud
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:30pm
- Exercise: Logging on to our Computerome cloud (Logging on to Cloud system)
- Peter Wad Sackett,Trine Zachariasen, Gabriel Renaud,
- 1:30pm-2:15pm
- Introduction to UNIX (Video lectures to watch from "Unix intro.." to "Touching upon...") (Exercises possible answers here) (Unix Notes)
- Peter Wad Sackett, Trine Zachariasen
- 2:15pm-2:30pm
- Break
- 2:30pm-3:30pm
- Introduction to UNIX (continued) (Video lectures to watch from "Unix intro.." to "Touching upon...") (Exercises possible answers here) (Unix Notes)
- Peter Wad Sackett, Trine Zachariasen
- 3:30pm-4:00pm
- First look at data (First look exercise)
- Peter Wad Sackett, Trine Zachariasen
Tueday, January 5
Data pre-processing & Alignment
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
- Shyam Gopalakrishnan, Trine Zachariasen
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Data pre-processing (Lecture slides) (Data Preprocess exercise) (Data Preprocess exercise answers)
- Shyam Gopalakrishnan
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:15pm
- Alignment (Lecture slides)
- Gabriel Renaud
- 2:15pm-2:30pm
- Break
- 2:30pm-4:00pm
- Exercise: Alignment (Alignment exercise) (Alignment exercise answers)
- Gabriel Renaud, Trine Zachariasen
Wednesday, January 6
Alignment & Genotyping
- 9:00am-9:30am
- Functional Human Variation
- Shyam Gopalakrishnan, (Lecture slides)
- 9:30am-10:00am
- Alignment postprocessing & variant calling (Lecture slides)
- Gabriel Renaud
- 10:00am-10:15am
- Break
- 10:15am-12:00pm
- Exercise: Postprocessing & variant calling (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise) (SNP_calling_exercise_answers)
- Gabriel Renaud, Trine Zachariasen
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: de novo assembly (Lecture slides)(Handout (TODO))
- Shyam Gopalakrishnan
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Shyam Gopalakrishnan, Trine Zachariasen
Thursday, January 7
Metagenomics
- 9:00am-9:45am
- Metagenomics & Binning (Lecture slides)
- Gisle Vestergaard
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: Kaiju: Taxonomic classification (Kaiju exercise) (Kaiju solution)
- Gisle Vestergaard
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: Quantitative Metagenomics (Lecture slides)
- Gisle Vestergaard
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: Quantitative Metagenomics (Exercise) (Solution)
- Gisle Vestergaard
Friday, January 8
Cell-free DNA and recap test
- 9:00am-9:45am
- Cell-free DNA (Lecture slides)
- Søren Besenbacher
- 9:45am-10:00am
- Break
- 10:00am-12:00am
- Exercise: Cell free DNA (cfDNA exercise)(CfDNA_exercise_answers)
- Søren Besenbacher, Trine Zachariasen
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Recap Test (Test 2021)(answers)
- Gabriel Renaud, Trine Zachariasen
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Time to work on this week's exercises
- Gabriel Renaud, Trine Zachariasen
Monday, January 11
RNA-seq and Cancer-seq
- 9:00am-9:45am
- Lecture: RNAseq (Lecture slides)
- Francesca Bertolini
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: RNAseq (Rnaseq_exercise) (Rnaseq_exercise_answers)
- Francesca Bertoloni, Trine Zachariasen
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: Cancer-seq (Lecture slides)
- Adrian Otamendi, Trine Zachariasen
- 2:00pm-4:00pm
- Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
- Adrian Otamendi, Trine Zachariasen
Tuesday, January 12
Genomic Epidemiology and tech talk
- 9:00am-9:55am
- Exercise: Genomic Epidemiology (Genomic epidemiology exercise) (Genomic epidemiology solution)
- Shyam Gopalakrishnan
- 9:55am-10:10am
- Break
- 10:10am-12:00pm
- Case story: Genomic Epidemiology (Lecture)
- Pimlapas Leekitecharoenphon (Shinny)
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:00pm
- Tech talk work
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
- 2:00pm-4:00pm
- TechTalks Presentations
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Wednesday, January 13
Ancient DNA & Project work
- 9:00am-10:00am
- Ancient DNA (Lecture slides)
- Martin Sikora
- 10:00am-10:15am
- Break
- 10:15am-12:00pm
- Exercise: Ancient DNA (Ancient DNA exercise) (Ancient_DNA_exercise_answers)
- Martin Sikora, Trine Zachariasen
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
- 1:45pm-4:00pm
- Projects & Group formation, prepare your presentation for tomorrow. please write group names in the document for 2021
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Thursday, January 14
Project presentation
- 9:00am-12:00pm
- Project work/Prepare presentations for this afternoon
- Please go to Discord for help, we will be available.
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:00pm
- Project Presentations (what you will do) /Project work
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
- 2:00pm-4:00pm
- Project work
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Friday, January 15
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Monday, January 18
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Tuesday, January 19
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Wednesday, January 20
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Thursday, January 21
Project Work & Poster Printing
- Produce a PDF of your poster, presentation will online this year.
- Poster guide & requirements
- 10:00am-12:00pm
- Q&A: Practical information about the Exam
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen
Friday, January 22
Poster session - Online
- 10:00am-2:00pm
- Poster session part (exam)