Program 2025: Difference between revisions

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Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 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.
Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 303A] in auditorium 44. Offline discussions will take place on Discord (https://discord.gg/7FX35qUmGX). Please register with your '''full name'''. Will use Discord for online classes and collaboration with your project partners.


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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'''.  
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 24th of January 2025'''.  




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=== Course Program - January 2024 ===
=== Course Program - January 2025 ===




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([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Exercises] possible answers [[Unix_answers|here]])  
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Exercises] possible answers [[Unix_answers|here]])  
([https://teaching.healthtech.dtu.dk/material/22126/UnixInstructions36610.pdf Unix Notes])</DD>
([https://teaching.healthtech.dtu.dk/22126/index.php/Unix_notes Unix Notes])</DD>
<DD>Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Video lectures to watch from "Unix intro.." to "Touching upon..."])  
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Exercises] possible answers [[Unix_answers|here]])
([https://teaching.healthtech.dtu.dk/22113/index.php/Unix Exercises] possible answers [[Unix_answers|here]])
([https://teaching.healthtech.dtu.dk/material/22126/UnixInstructions36610.pdf Unix Notes])</DD>
([https://teaching.healthtech.dtu.dk/22126/index.php/Unix_notes Unix Notes])</DD>
<DD>Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<HR>
<HR>


''Alignment & Genotyping & de novo assembly''
''Variant calling ''
<DL>
<DL>
<DT>9:00am-9:30am</DT>
<DT>9:00am-9:30am</DT>
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'''Thursday, January 9'''
'''Thursday, January 9'''
<HR>
<HR>
''Ancient DNA and RNAseq''
''Assembly, annotation and long read sequencing''


<DL>
<DL>


<DT>9:00am-10:00pm</DT>
<DT>9:00am-10:00pm</DT>
<DD>Lecture: de novo assembly ([https://teaching.healthtech.dtu.dk/material/22126/2024/43_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Lecture: de novo assembly and genomic annotations ([https://teaching.healthtech.dtu.dk/material/22126/2024/43_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD>
<DD>Martin Sikora</DD>
<DD>Gabriel Renaud</DD>


<DT>10:00pm-10:15pm</DT>
<DT>10:00pm-10:15pm</DT>
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<DT>10:15pm-12:00pm</DT>
<DT>10:15pm-12:00pm</DT>
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD>
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD>
<DD>Martin Sikora, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
 
 
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>
 
 
<DL>
<DT>1:00pm-2:00pm </DT>
<DD>Lecture: Long read sequencing ([https://teaching.healthtech.dtu.dk/material/22126/2024/Long_read_sequencing_Lecture_08-01-2023.pdf Lecture slides])</DD>
<DD>Frederikke Pedersen</DD>
 
<DT>2:00am-2:15pm</DT>
<DD>''Break''</DD>
 
<DT>2:15pm-4:00pm</DT>
<DD>Exercise: Long read technology ([[longread exercise]])([[longread_exercise_answers]])</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<BR>


<BR>


<HR>
'''Friday, January 10'''
<HR>
''Ancient DNA and recap test''


<DT>9:00am-10:00pm</DT>
<DT>9:00am-10:00pm</DT>
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<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD>
<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD>
<DD>Martin Sikora, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>Martin Sikora, Amanda Gammelby Qvesel, Mads Hartmann</DD>




<DT>12:00pm-1:00pm </DT>
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>
<DD>''Lunch Break'' </DD>


<DT>1:00pm-1:45pm</DT>
<DT>1:00pm-1:45pm</DT>
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<DD>Exercise: RNAseq ([[Rnaseq_exercise]])  ([[Rnaseq_exercise_answers]]) </DD>
<DD>Exercise: RNAseq ([[Rnaseq_exercise]])  ([[Rnaseq_exercise_answers]]) </DD>
<DD>Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Kristoffer Vitting-Seerup, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<BR>
<BR>
<HR>
'''Friday, January 10'''
<HR>
''Long read tech and recap test''
<DL>
<DT>9:00am-9:45am </DT>
<DD>Lecture: Long read sequencing ([https://teaching.healthtech.dtu.dk/material/22126/2024/Long_read_sequencing_Lecture_08-01-2023.pdf Lecture slides])</DD>
<DD>Frederikke Pedersen</DD>
<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>
<DT>10:00am-12:00am</DT>
<DD>Exercise: Long read technology ([[longread exercise]])([[longread_exercise_answers]])</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DT>12:00pm-1:00pm </DT>
<DD>''Lunch Break'' </DD>




<DT>1:00pm-1:45pm</DT>
<DT>1:00pm-1:45pm</DT>
<DD>Brief presentation on annotation & Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024.pdf Test 2024])([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024_withA.pdf answers])</DD>
<DD>Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024.pdf Test 2024])([https://teaching.healthtech.dtu.dk/material/22126/2024/test_2024_withA.pdf answers])</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann </DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann </DD>


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<DT>2:00pm-4:00pm</DT>
<DT>2:00pm-4:00pm</DT>
<DD>Time to work on this week's exercises</DD>
<DD>Time to catch up on this week's exercises</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>
</DL>
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<HR>
<HR>


<HR>
''Metagenomics''
''Metagenomics''
<DL>
<DL>
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<DT>1:45pm-4:00pm </DT>   
<DT>1:45pm-4:00pm </DT>   
<DD>Projects & Group formation, prepare an outline for tomorrow. please write group names in the [https://docs.google.com/document/d/1WTclnPWBoS1JvZ2C1qoshooQhuVEogVg3ZHGKaQt0l0/edit?usp=sharing document for 2024]</DD>
<DD>Projects & Group formation, prepare an outline for tomorrow. please write group names in the [https://docs.google.com/document/d/11paeLyAagaIB9ytUq9ZQUaLUF8nELlt_-oxpeErFm_s/edit?usp=sharing document for 2025]</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
<DD>Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann</DD>
</DL>
</DL>

Latest revision as of 15:23, 15 November 2024

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/7FX35qUmGX). 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 24th of January 2025.


For the laptop if you have a secure laptop (e.g. work laptop from Statens Serum Institut for instance), please bring your personal laptop.


Course Program - January 2025

Monday, January 6

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, Amanda Gammelby Qvesel, Mads Hartmann, 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, Amanda Gammelby Qvesel, Mads Hartmann, 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, Amanda Gammelby Qvesel, Mads Hartmann
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, Amanda Gammelby Qvesel, Mads Hartmann
3:30pm-4:00pm
First look at data (First look exercise)
Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann
3:30pm-4:00pm
If you are done, some UNIX with zip codes (Zip codes)
Peter Wad Sackett, Amanda Gammelby Qvesel, Mads Hartmann


Tuesday, January 7

Data pre-processing & Alignment

9:00am-10:45am
Data basics (Lecture slides) (Data basics exercise) (Data basics exercise answers)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
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, Amanda Gammelby Qvesel, Mads Hartmann

Wednesday, January 8

Variant calling

9:00am-9:30am
Functional Human Variation
Gabriel Renaud, (Lecture slides)
9:30am-10:15am
Variant calling part 1 (Lecture slides)
Gabriel Renaud
10:15am-10:30am
Break
10:30am-12:00pm
Exercise: variant calling part 1 (Postprocess exercise) (Postprocess_exercise_answers) (SNP calling exercise) (SNP_calling_exercise_answers)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
12:00pm-1:00pm
Lunch Break
1:00pm-1:45pm
Lecture: variant calling part 2 (Lecture slides)(Handout)
Gabriel Renaud
1:45pm-2:00pm
Break
2:00pm-4:00pm
Exercise: variant calling part 2 (denovo exercise) (denovo solution)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Thursday, January 9

Assembly, annotation and long read sequencing

9:00am-10:00pm
Lecture: de novo assembly and genomic annotations (Lecture slides)(Handout)
Gabriel Renaud
10:00pm-10:15pm
Break
10:15pm-12:00pm
Exercise: de novo assembly (denovo exercise) (denovo solution)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
12:00pm-1:00pm
Lunch Break
1:00pm-2:00pm
Lecture: Long read sequencing (Lecture slides)
Frederikke Pedersen
2:00am-2:15pm
Break
2:15pm-4:00pm
Exercise: Long read technology (longread exercise)(longread_exercise_answers)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Friday, January 10

Ancient DNA and recap test

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, Amanda Gammelby Qvesel, Mads Hartmann
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, Amanda Gammelby Qvesel, Mads Hartmann
1:00pm-1:45pm
Recap Test (Test 2024)(answers)
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann
1:45pm-2:00pm
Break
2:00pm-4:00pm
Time to catch up on this week's exercises
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann



Monday, January 13

Metagenomics

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, Amanda Gammelby Qvesel
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, Amanda Gammelby Qvesel


Tuesday, January 14

Genomic Epidemiology and group project

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, Amanda Gammelby Qvesel, Mads Hartmann
1:45pm-4:00pm
Projects & Group formation, prepare an outline for tomorrow. please write group names in the document for 2025
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Wednesday, January 15

CancerSeq & Project work

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, Amanda Gammelby Qvesel, Mads Hartmann
12:00pm-1:00pm
Lunch Break
1:00pm-4:00pm
Project consulation
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann

Thursday, January 16

Project presentation

9:00am-12:00pm
Project work
12:00pm-1:00pm
Lunch Break
1:00pm-4:00pm
Project work
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Friday, January 17

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Monday, January 20

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Tuesday, January 21

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Wednesday, January 22

Project work

9:00am-4:00pm
Project work
1:00pm-3:00pm
Project work/Office hours
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Thursday, January 23

Project Work & Produce 1 page report

10:00am-12:00pm
Q&A: Practical information about the exam
Project work/Office hours
Gabriel Renaud, Amanda Gammelby Qvesel, Mads Hartmann


Friday, January 24

Exam

9:00am-4:00pm
Written Exam
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