Program 2024
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REMEMBER TO BRING A LAPTOP FOR EXERCISES
Lectures will be in person in building 303A in auditorium 44. Offline discussions will take place on Discord (https://discord.gg/7PKuKhKYQJ). 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 19th of January 2024.
Course Program - January 2024
Tuesday, January 2
Introduction - Next Generation Sequencing
- 9:00am-9:30am
- Introduction to course (Lecture slides)
- 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
- Exercise: Logging on to our pupil servers (Logging on to pupil system)
- Peter Wad Sackett, Astrid Brix Saksager, Grigorii Nos, Gabriel Renaud
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:30pm
- Exercise: Logging on to our pupil servers (Logging on to pupil system)
- Peter Wad Sackett, Astrid Brix Saksager, Grigorii Nos, 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, Astrid Brix Saksager, Grigorii Nos
- 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, Astrid Brix Saksager, Grigorii Nos
- 3:30pm-4:00pm
- First look at data (First look exercise)
- Peter Wad Sackett, Astrid Brix Saksager, Grigorii Nos
- 3:30pm-4:00pm
- If you are done, some UNIX with zip codes (Zip codes)
- Peter Wad Sackett, Astrid Brix Saksager, Grigorii Nos
Wednesday, January 3
Data pre-processing & Alignment
- 9:00am-10:45am
- Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 10:45am-11:00am
- Break
- 11:00am-12:00pm
- Data pre-processing (Lecture slides) (Data Preprocess exercise) (Data Preprocess exercise answers)
- Gabriel Renaud
- 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, Astrid Brix Saksager, Grigorii Nos
- 9:00am-9:30am
- Functional Human Variation
- Gabriel Renaud, (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, Astrid Brix Saksager, Grigorii Nos
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: de novo assembly (Lecture slides)(Handout)
- Gabriel Renaud
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-10:00pm
- Ancient DNA (Lecture slides)
- Martin Sikora
- 10:00pm-10:15pm
- Break
- 10:15pm-12:00pm
- Exercise: Ancient DNA (Ancient DNA exercise) (Ancient_DNA_exercise_answers)
- Martin Sikora, Astrid Brix Saksager, Grigorii Nos
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Lecture: RNAseq (Lecture slides) (Lecture slides with solutions)
- Kristoffer Vitting-Seerup
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: RNAseq (Rnaseq_exercise) (Rnaseq_exercise_answers)
- Kristoffer Vitting-Seerup, Astrid Brix Saksager, Grigorii Nos
- 9:00am-9:45am
- Lecture: Long read sequencing (Lecture slides)
- Frederikke Pedersen
- 9:45am-10:00am
- Break
- 10:00am-12:00am
- Exercise: Long read technology (longread exercise)(longread_exercise_answers)
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Brief presentation on annotation & Recap Test (Test 2024)(answers)
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Time to work on this week's exercises
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-9:45am
- Metagenomics & Binning (Lecture slides)
- Trine Zachariasen
- 9:45am-10:00am
- Break
- 10:00am-12:00pm
- Exercise: Kaiju: Taxonomic classification (Kaiju exercise) (Kaiju solution)
- Trine Zachariasen, Cecilie Thystrup, Astrid Brix Saksager
- 1:00pm-1:45pm
- Lecture: Quantitative Metagenomics (Lecture slides)
- Trine Zachariasen
- 1:45pm-2:00pm
- Break
- 2:00pm-4:00pm
- Exercise: Quantitative Metagenomics (QuantitativeMetagenomics) (QuantitativeMetagenomicsSolution)
- Trine Zachariasen, Cecilie Thystrup, Astrid Brix Saksager
- 9:00am-9:55am
- Case story: Genomic Epidemiology (Lecture)
- Pimlapas Leekitecharoenphon (Shinny)
- 9:55am-10:10am
- Break
- 10:10am-12:00pm
- Exercise: Genomic Epidemiology (Genomic epidemiology exercise) (Genomic epidemiology solution)
- Gabriel Renaud
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-1:45pm
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 1:45pm-4:00pm
- Projects & Group formation, prepare an outline for tomorrow. please write group names in the document for 2024
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-9:45am
- Lecture: Cancer-seq (Lecture slides)
- Elena Papaleo
- 10:00am-12:00pm
- Exercise: Cancer-seq (Cancerseq_exercise) (Cancerseq_exercise_answers)
- Matteo Arnaudi, Astrid Brix Saksager, Grigorii Nos
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project consulation
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-12:00pm
- Project work
- 12:00pm-1:00pm
- Lunch Break
- 1:00pm-4:00pm
- Project work
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-4:00pm
- Project work
- 1:00pm-3:00pm
- Project work/Office hours
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 10:00am-12:00pm
- Q&A: Practical information about the exam
- Project work/Office hours
- Gabriel Renaud, Astrid Brix Saksager, Grigorii Nos
- 9:00am-4:00pm
- Written Exam
Thursday, January 4
Alignment & Genotyping & de novo assembly
Friday, January 5
Ancient DNA and RNAseq
Saturday, January 6
Reading at home
Monday, January 8
Long read tech and recap test
Tuesday, January 9
Metagenomics
Wednesday, January 10
Genomic Epidemiology and project group
Thursday, January 11
CancerSeq & Project work
Friday, January 12
Project presentation
Monday, January 15
Project work
Tuesday, January 16
Project work
Wednesday, January 17
Project work
Thursday, January 18
Project work
Thursday, January 18
Project Work & Produce 1 page report
Friday, January 19
Exam