Program 2020
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REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES
Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, Building 210, Room H162 in Lyngby (map).
The courses has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Friday 24th 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 2020
Monday, January 6
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)
- 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, Bernadette Kofoed Christiansen, Nanna Møller Barnkob
- 1:30pm-2:15pm
- Introduction to UNIX (Lecture slides) (Exercise) (Unix Notes)
- Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob
- 2:15pm-2:30pm
- Break
- 2:30pm-3:30pm
- Introduction to UNIX (Lecture slides) (Exercise) (Unix Notes)
- Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob
- 3:30pm-4:00pm
- First look at data (First look exercise)
- Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob
Tueday, January 7
Data pre-processing & Genomic Epidemiology
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics solution)
- Shyam Gopalakrishnan, Bernadette Kofoed Christiansen, Freja Dahl Hede
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Data pre-processing (Lecture slides) (Data Preprocess exercise) (Data Preprocess solution)
- Shyam Gopalakrishnan, Bernadette Kofoed Christiansen, Freja Dahl Hede
- 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 solution)
- Gabriel Renaud, Bernadette Kofoed Christiansen, Freja Dahl Hede
Wednesday, January 8
Alignment & Genotyping
- 9:00am-9:30am
- Functional Human Variation
- Adrian Otamendi Laspiur, (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 solution) (SNP calling exercise) (SNP calling solution)
- Gabriel Renaud, TBA
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:15pm
- Ancient DNA (Lecture slides)
- Gabriel Renaud
- 2:15pm-2:30pm
- Break
- 2:30pm-4:00pm
- Exercise: Ancient DNA (Ancient DNA exercise)
- Gabriel Renaud, TBA
Thursday, January 9
de novo assembly & Metagenomics
- 9:00am-9:45am
- Lecture: de novo assembly (Lecture slides) (Handout)
- Shyam Gopalakrishnan
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Shyam Gopalakrishnan, Nanna Møller Barnkob
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Metagenomics & Binning (Lecture slides)
- Gisle Vestergaard
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: Metagenomic de novo assembly (Metagenomic assembly exercise) (Metagenomic assembly solution)
- Gisle Vestergaard
Friday, January 10
Quantitative Metagenomics and Test
- 9:00am-9:45am
- Lecture: Quantitative Metagenomics (Lecture slides)
- Gisle Vestergaard
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: Quantitative Metagenomics (Exercise) (Solution)
- Gisle Vestergaard
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Recap Test (Test)
- Gabriel Renaud, Line Egerod Lund
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Time to work on this week's exercises
- Gabriel Renaud, Line Egerod Lund
Monday, January 13
RNA-seq and Cancer-seq
Tuesday, January 14
Wednesday, January 15
Project work
- 9:00am-9:45am
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund
- 9:45am-10:45am
- Projects & Group formation, please write group names in the document
- Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Project work
- Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project work/Prepare presentations for tomorrow How to get to Gabriel/Shyam/Gisle office: first go to 202, go to the 3rd floor and go to building 204 via the skyway. We are in 252/251
Thurday, January 16
Project work & Project Presentations
- 9:00am-12:00pm
- Project work
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:00pm
- Project Presentations
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Friday, January 17
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Monday, January 20
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Tueday, January 21
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Wednesday, January 22
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Thurday, January 23
Project Work & Poster Printing
- Print your poster, it is possible to print in DTU library for 16-30kr.
- Poster guide & requirements
- 10:00am-12:00pm
- Q&A: Practical information about the Exam
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, TBA
Friday, January 24
Poster session - in the hall of TBA
- 10:00am-2:00pm
- Poster session part (exam)