Program 2022
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REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES
Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). 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 21st of January.
Course Program - January 2022
Monday, January 3
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 2022)
- 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,Josh Rubin, Nicola Vogel, 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, Josh Rubin, Nicola Vogel
- 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, Josh Rubin, Nicola Vogel
- 3:30pm-4:00pm
- First look at data (First look exercise)
- Peter Wad Sackett, Josh Rubin, Nicola Vogel
Tueday, January 4
Data pre-processing & Alignment
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
- Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
- 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-2:45pm
- Brief reminder on probabilities and Bayesian theory (Lecture slides)
- Gabriel Renaud
- 2:45pm-4:00pm
- Exercise: Alignment (Alignment exercise) (Alignment exercise answers)
- Gabriel Renaud, Josh Rubin, Nicola Vogel
Wednesday, January 5
Alignment & Genotyping
- 9:00am-9:30am
- Functional Human Variation
- Shyam Gopalakrishnan, (Lecture slides)
- 9:30am-10:15am
- Alignment postprocessing & variant calling (Lecture slides)
- Gabriel Renaud
- 10:15am-10:30am
- Break
- 10:30am-12:00pm
- Exercise: Postprocessing & variant calling (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise) (SNP_calling_exercise_answers)
- Gabriel Renaud, Josh Rubin, Nicola Vogel
- 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, Josh Rubin, Nicola Vogel
Thursday, January 6
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,Trine Zachariasen
- 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, Trine Zachariasen
Friday, January 7
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, Josh Rubin, Nicola Vogel
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Recap Test (Test 2021)(answers)
- Gabriel Renaud, Josh Rubin, Nicola Vogel
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Time to work on this week's exercises
- Gabriel Renaud, Josh Rubin, Nicola Vogel
Monday, January 10
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, Josh Rubin, Nicola Vogel
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: Cancer-seq (Lecture slides)
- Elena Papaleo
- 2:00pm-4:00pm
- Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
- Adrian Otamendi, Josh Rubin, Nicola Vogel
Tuesday, January 11
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, Josh Rubin, Nicola Vogel
- 2:00pm-4:00pm
- TechTalks Presentations
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Wednesday, January 12
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, Josh Rubin, Nicola Vogel
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
- 1:45pm-4:00pm
- Projects & Group formation, prepare your presentation for tomorrow. please write group names in the document for 2022
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Thursday, January 13
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, Josh Rubin, Nicola Vogel
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-2:00pm
- Project Presentations (what you will do) /Project work
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
- 2:00pm-4:00pm
- Project work
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Friday, January 14
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Monday, January 17
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Tuesday, January 18
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Wednesday, January 19
Project work
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel
Thursday, January 20
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, Josh Rubin, Nicola Vogel
Friday, January 21
Poster session - Online
- 9:00am-4:00pm
- Poster session part (exam)