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Next Generation Sequencing Analysis - #27626
The course will be held from June 10th - 28th, 2013
Tentative programme
Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, room 062 in Lyngby (map).
The courses has two tracks, the first half is lectures and exercises and the last half is project work ending with exam on Friday 28nd of June.
Course Programme - June 2013
Monday, June 10
Introduction - Next Generation Sequencing
- 9.00-9.30
- Introduction to course & Pre-test
(Lecture slides)
(Pre-test)
- Simon Rasmussen
- 9.30-10.00
- Introduction to NGS
(Lecture slides)
- Simon Rasmussen
- 10.00-10.45
- 2nd and 3rd generation NGS Technologies
(Lecture slides)
- Morten Rasmussen
- 10.45-11.00
- Break
- 11.00-12.00
- Tech talk group formation and group work
(Lecture slides)
- Simon Rasmussen
- 12.00-13.00
- Lunch Break
- 13.00-13.30
- Exercise: Logging on to the CBS system
(Logging on to CBS system)
- Simon Rasmussen, Jens Friis-Nielsen, Dhany Saputra
- 13.30-14.15
- Introduction to UNIX
(Exercise)
(Unix Notes)
- Peter Wad Sackett, Simon Rasmussen, Jens Friis-Nielsen
- 14.15-14.30
- Break
- 14.30-15.30
- Introduction to UNIX
(Exercise)
(Unix Notes)
- Peter Wad Sackett, Simon Rasmussen, Jens Friis-Nielsen
- 15.30-16.00
- First look at data
(Exercise)
- Simon Rasmussen, Jens Friis-Nielsen
Tuesday, June 11
Tech talk & Alignment
- 9.00-10.45
- Tech talk work & presentations
- Tech talk presentations
- Simon Rasmussen
- 10.45-11.00
- Break
- 11.00-14.00
- Exercise: Labster Exercise
- Mikkel Morsing (Labster), Simon Rasmussen, Aviaja Hauptmann, Ida Bonde, Asli Ozen
- Remember to take your lunch break!
- 14.00-14.30
- Data basics
(Lecture slides)
(Exercise)
(Solution)
- Simon Rasmussen, Asli Ozen, Damian Plichta
- 14.30-15.45
- Data pre-processing
(Lecture slides)
(Exercise)
(Solution)
- Simon Rasmussen, Asli Ozen, Damian Plichta
- 15.45-16.00
- Wrap-up (Recap points)
- Simon Rasmussen
Wednesday, June 12
Alignment & Genotyping
- 9.00-9.45
- Alignment
(Lecture slides)
- Simon Rasmussen
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: Alignment
(Exercise)
(Solution)
- Simon Rasmussen, Asli Ozen, Dhany Saputra, Damian Plichta
- 12.00-13.00
- Lunch Break
- 13.00-13.15
- Functional Human Variation
- Agata Wesolowska-Andersen(Lecture slides)
- 13.15-13.45
- Alignment postprocessing & variant calling
(Lecture slides)
(Handout)
- Natasja Ehlers
- 13.45-14.00
- Break
- 14.00-15.45
- Exercise: Postprocessing & variant calling
(Preprocess Exercise)
(Preprocess solutions)
(SNP calling Exercise)
(SNP calling solutions)
- Simon Rasmussen, Natasja Ehlers, Agata Wesolowska-Andersen, Txema Izarzugaza
- 15.45-16.00
- Wrap-up
- Simon Rasmussen
Thursday, June 13
de novo assembly & Metagenomics
- 9.00-9.45
- Lecture: de novo assembly
(Lecture slides)
- Simon Rasmussen, Asli Ozen, Damian Plichta, Dhany Saputra
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: de novo assembly
(Exercise)
(Solution)
- Simon Rasmussen, Asli Ozen, Damian Plichta, Dhany Saputra
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Metagenomics
(Lecture slides (AG))
(Lecture slides (SR))
- Agnieszka Juncker, Simon Rasmussen
- 13.45-14.00
- Break
- 14.00-15.45
- Exercise: Metagenomic de novo assembly
(Exercise)
(Solution)
- Simon Rasmussen, Josef Vogt, Jens Friis-Nielsen
- 15.45-16.00
- Wrap-up
- Simon Rasmussen
Friday, June 14
Metagenomics and Recap session
- 9.00-9.45
- Lecture: Quantitative Metagenomics
(Lecture slides)
- Henrik Bjorn Nielsen
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: Quantitative Metagenomics
(Exercise)
- Henrik Bjorn Nielsen, Damian Plichta, Simon Rasmussen
- 12.00-13.00
- Lunch Break
- 13.00-13.30
- Recap Lecture
(Lecture slides)
- Simon Rasmussen
- 13.30-15.30
- Time to work on this weeks exercises
- Simon Rasmussen
Monday, June 17
Chip-seq and Genomic Epidemiology
- 9.00-9.45
- Lecture: ChIP-seq
(Lecture slides)
- Federico De Masi
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: ChIP-seq
(Exercise)
- Federico De Masi, Simon Rasmussen, Damian Plichta
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Case story: Genomic Epidemiology
(Lecture)
- Frank Aarestrup, Danish National Food Institute, Technical University of Denmark
- 13.45-14.00
- Break
- 14.00-15.45
- Exercise: Genomic Epidemiology
(Exercise)
(Solution)
- Rolf Kaas, Dhany Saputra, Simon Rasmussen
- 15.45-16.00
- Wrap-up
- Simon Rasmussen
Tuesday, June 18
RNAseq & Ancient DNA
- 9.00-9.45
- Lecture: RNAseq
(Lecture slides)
- Francesco Favero
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: RNAseq
(Exercise)
- Francesco Favero, Simon Rasmussen, Dhany Saputra
- 12.00-13.00
- Lunch Break
- 13.00-13.30
- Ancient DNA
(Lecture slides)
- Aurelien Ginolhac, Hakon Jonsson
- 13.30-15.45
- Exercise: Ancient DNA
(Exercise pdf)
(Exercise txt)
- Aurelien Ginolhac, Hakon Jonsson, Simon Rasmussen
- 15.15-15.30
- Wrap-up
- Simon Rasmussen
Wednesday, June 19
Project work
- 9.00-9.45
- Projects & Group formation
(Lecture slides)
- Simon Rasmussen
- 9.45-10.45
- Projects & Group formation
- Simon Rasmussen
- 10.45-11.00
- Break
- 11.00-12.00
- Project work
- Simon Rasmussen
- 12.00-13.00
- Lunch Break
- 13.00-16.00
- Project work
- Simon Rasmussen
Thursday, June 20
Project work & Project Presentations
- 9.00-10.00
- Project presentations
- Simon Rasmussen
- 10.00-12.00
- Project work
- Simon Rasmussen
- 12.00-13.00
- Lunch Break
- 13.00-16.00
- Project work
- Simon Rasmussen
Friday, June 21
Project work
- 9.00-16.00
- Project work
- Simon Rasmussen
Monday, June 24
Project work
- 9.00-16.00
- Project work
- Simon Rasmussen
Tuesday, June 25
Project work
- 9.00-16.00
- Project work
- Simon Rasmussen
Wednesday, June 26
Project work
- 9.00-16.00
- Project work
- Simon Rasmussen
Thursday, June 27
Poster Printing
- 14.00
- Deadline for paying Simon Rasmussen Dkr 250 for poster printing and sending poster files (pdf) to Simon Rasmussen
- Poster guide & requirements
Friday, June 28
Poster session - in the hall in front of CBS (building 208)
- 10.00-12.00
- Poster session part I (exam)
- 12.00-13.00
- Lunch Break
- 13.00-15.00
- Poster session part II (exam)
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This file was last modified Tuesday 18th 2013f June 2013 07:06:11 GMT |
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