WikiSysop: Created page with " Lectures and exercises will take place on Discord (https://discord.gg/JxV3pHyHgV). 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 22th of January. This term, we will be using Piazza for class dis..."

2024-03-19T16:06:46Z

Created page with "  Lectures and exercises will take place on Discord (https://discord.gg/JxV3pHyHgV). 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 22th of January. This term, we will be using Piazza for class dis..."

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Lectures and exercises will take place on Discord (https://discord.gg/JxV3pHyHgV). 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 22th 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 [https://piazza.com/class/kjernxm6wre7ck here]

=== Course Program - January 2021 ===

<HR>
'''Monday, January 4'''
<HR>
''Introduction - Next Generation Sequencing''
<DL>
<DT>9:00am-9:30am</DT>
<DD>Introduction to course & Pre-test
([https://teaching.healthtech.dtu.dk/material/22126/2021/11_Introduction_to_course_GR.pdf Lecture slides])
([https://teaching.healthtech.dtu.dk/material/22126/2021/1_pre-test_2021.pdf Pre-test])</DD>
<DD>Gabriel Renaud</DD>

<DT>9:30am-10:00am</DT>
<dd>Introduction to NGS
([https://teaching.healthtech.dtu.dk/material/22126/2021/12_Introduction_to_NGS_GR.pdf Lecture slides]) </DD>
<DD>Gabriel Renaud</DD>

<DT>10:00am-10:45am</DT>
<DD>2nd and 3rd generation NGS Technologies
([https://teaching.healthtech.dtu.dk/material/22126/2021/13_Introduction_to_NGS_technology_GR.pdf Lecture slides])</DD>
<DD>Gabriel Renaud</DD>

<DT>10:45am-11:00am</DT>
<DD>''Break''</DD>

<DT>11:00am-12:00pm</DT>
<DD>Tech talk group formation and group work
([https://teaching.healthtech.dtu.dk/material/22126/2021/14_Tech_Talks_GR.pdf Lecture slides])
([https://docs.google.com/spreadsheets/d/1Ul_sb43hdxCkenJM9rEPzudyXVWtZVxwIZrxgan9Z_g/edit?usp=sharing Student Groups 2021]) </DD>
<DD>Gabriel Renaud</DD>

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

<DT>1:00pm-1:30pm</DT>
<DD>Exercise: Logging on to our Computerome cloud ([[Logging on to Cloud system]])</DD>
<DD>Peter Wad Sackett,Trine Zachariasen, Gabriel Renaud, </DD>

<DT>1:30pm-2:15pm </DT>
<DD>Introduction to UNIX
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."])
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]])
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD>
<DD>Peter Wad Sackett, Trine Zachariasen </DD>

<DT>2:15pm-2:30pm</DT>
<DD>''Break''</DD>

<DT>2:30pm-3:30pm </DT>
<DD>Introduction to UNIX (continued)
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."])
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]])
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD>
<DD>Peter Wad Sackett, Trine Zachariasen </DD>

<DT>3:30pm-4:00pm </DT>
<DD>First look at data
([[First look exercise]])
<DD>Peter Wad Sackett, Trine Zachariasen</DD>
</DL>

 

<HR>
'''Tueday, January 5'''
<HR>
''Data pre-processing & Alignment''

<DL>
<DT>9:00am-10:45am </DT>
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2021/2_Data_Basics_SG.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD>
<DD>Shyam Gopalakrishnan, Trine Zachariasen</DD>

<DT>10:45am-11:00am</DT>
<DD>''Break''</DD>

<DT>11:00am-12:00pm </DT>
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2021/2_Data_preprocessing_SG.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD>
<DD>Shyam Gopalakrishnan </DD>

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

<DT>1:00pm-2:15pm</DT>
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2021/23_Alignment_GR.pdf Lecture slides]) </DD>
<DD>Gabriel Renaud </DD>

<DT>2:15pm-2:30pm</DT>
<DD>''Break'' </DD>

<DT>2:30pm-4:00pm</DT>
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD>
<DD>Gabriel Renaud, Trine Zachariasen</DD>
</DL>

 

<HR>
'''Wednesday, January 6'''
<HR>

''Alignment & Genotyping''
<DL>
<DT>9:00am-9:30am</DT>
<DD>Functional Human Variation</DD>
<DD>Shyam Gopalakrishnan, ([https://teaching.healthtech.dtu.dk/material/22126/2021/FunctionalHumanVariation_SG.pdf Lecture slides])</DD>

<DT>9:30am-10:00am</DT>
<DD>Alignment postprocessing & variant calling ([https://teaching.healthtech.dtu.dk/material/22126/2021/41_post_alignment_variantcalling_GR.pdf Lecture slides])</DD>

<DD>Gabriel Renaud</DD>

<DT>10:00am-10:15am</DT>
<DD>''Break''</DD>

<DT>10:15am-12:00pm</DT>
<DD>Exercise: Postprocessing & variant calling ([[Postprocess exercise]]) ([[Postprocess_exercise_answers]]) ([[SNP calling exercise]]) ([[SNP_calling_exercise_answers]])</DD>
<DD>Gabriel Renaud, Trine Zachariasen </DD>

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

<DT>1:00pm-1:45pm </DT>
<DD>Lecture: de novo assembly ([https://teaching.healthtech.dtu.dk/material/22126/2021/4_de_novo_assembly_course_SG.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout (TODO)]) </DD>
<DD>Shyam Gopalakrishnan</DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break''</DD>

<DT>2:00pm-4:00pm</DT>
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD>
<DD>Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

<HR>
'''Thursday, January 7'''
<HR>
''Metagenomics''
<DL>
<DT>9:00am-9:45am </DT>
<DD>Metagenomics & Binning ([https://teaching.healthtech.dtu.dk/material/22126/2021/Metagenomics_binning.pdf Lecture slides])</DD>
<DD>Gisle Vestergaard</DD>

<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>

<DT>10:00am-12:00pm</DT>
<DD>Exercise: Kaiju: Taxonomic classification ([[Kaiju exercise]]) ([[Kaiju solution]]) </DD>
<DD>Gisle Vestergaard</DD>

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

<DT>1:00pm-1:45pm</DT>
<DD>Lecture: Quantitative Metagenomics ([https://teaching.healthtech.dtu.dk/material/22126/2021/Quantitative_metagenomics.pdf Lecture slides])</DD>
<DD>Gisle Vestergaard</DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break''</DD>

<DT>2:00pm-4:00pm</DT>
<DD>Exercise: Quantitative Metagenomics ([http://teaching.healthtech.dtu.dk/22126/index.php/QuantitativeMetagenomics Exercise]) ([http://teaching.healthtech.dtu.dk/22126/index.php/QuantitativeMetagenomicsSolution Solution]) </DD>
<DD>Gisle Vestergaard</DD>
</DL>

 

<HR>
'''Friday, January 8'''
<HR>
''Cell-free DNA and recap test''
<DL>
<DT>9:00am-9:45am </DT>
<DD>Cell-free DNA ([https://teaching.healthtech.dtu.dk/material/22126/2021/cfDNA_lecture_2020_SB.pdf Lecture slides])</DD>
<DD>Søren Besenbacher</DD>

<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>

<DT>10:00am-12:00am</DT>
<DD>Exercise: Cell free DNA ([[cfDNA exercise]])([[CfDNA_exercise_answers]])</DD>
<DD>Søren Besenbacher, Trine Zachariasen</DD>

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

<DT>1:00pm-1:45pm</DT>
<DD>Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2021/test_2021.pdf Test 2021])([https://teaching.healthtech.dtu.dk/material/22126/2021/test_2021_withA.pdf answers])</DD>
<DD>Gabriel Renaud, Trine Zachariasen </DD>

<DT>1:45pm-2:00pm</DT>
<DD>''Break''</DD>

<DT>2:00pm-4:00pm</DT>
<DD>Time to work on this week's exercises</DD>
<DD>Gabriel Renaud, Trine Zachariasen</DD>
</DL>

 

<HR>
'''Monday, January 11'''
<HR>

''RNA-seq and Cancer-seq''
<DL>

<DT>9:00am-9:45am</DT>
<DD>Lecture: RNAseq ([https://teaching.healthtech.dtu.dk/material/22126/2021/RNA-seq%2011-01-2021.pdf Lecture slides])</DD>
<DD>Francesca Bertolini</DD>

<DT>9:45am-10:00am</DT>
<DD>''Break''</DD>

<DT>10:00am-12:00pm</DT>
<DD>Exercise: RNAseq ([[Rnaseq_exercise]]) ([[Rnaseq_exercise_answers]]) </DD>
<DD>Francesca Bertoloni, Trine Zachariasen </DD>

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

<DT>1:00pm-1:45pm </DT>
<DD>Lecture: Cancer-seq ([https://teaching.healthtech.dtu.dk/material/22126/2021/CancerGenomics_Izarzugaza%20copy.pdf Lecture slides]) </DD>
<DD>Adrian Otamendi, Trine Zachariasen </DD>

<DT>2:00pm-4:00pm</DT>
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD>
<DD>Adrian Otamendi, Trine Zachariasen </DD>
</DL>

 

<HR>
'''Tuesday, January 12'''
<HR>

''Genomic Epidemiology and tech talk''

<DL>
<DT>9:00am-9:55am</DT>
<DD>Exercise: Genomic Epidemiology ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD>
<DD>Shyam Gopalakrishnan</DD>

<DT>9:55am-10:10am</DT>
<DD>''Break''</DD>

<DT>10:10am-12:00pm</DT>
<DD>Case story: Genomic Epidemiology ([https://teaching.healthtech.dtu.dk/material/22126/2021/Genomic_epidemiology_NGScourse_Jan2021.pdf Lecture])</DD>
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD>

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

<DT>1:00pm-2:00pm </DT>
<DD>Tech talk work</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen </DD>

<DT>2:00pm-4:00pm </DT>
<DD>TechTalks Presentations</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen </DD>

</DL>

 

<HR>
'''Wednesday, January 13'''
<HR>
''Ancient DNA & Project work''

<DL>
<DT>9:00am-10:00am</DT>
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2021/dtu_adna_2021.pdf Lecture slides])</DD>
<DD>Martin Sikora</DD>

<DT>10:00am-10:15am</DT>
<DD>''Break''</DD>

<DT>10:15am-12:00pm</DT>
<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD>
<DD>Martin Sikora, Trine Zachariasen</DD>

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

<DT>1:00pm-1:45pm </DT>
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2021/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/posters.tar.gz Examples from previous courses]) </DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>

<DT>1:45pm-4:00pm </DT>
<DD>Projects & Group formation, prepare your presentation for tomorrow. please write group names in the [https://docs.google.com/document/d/1xVCMb6wQdqsX4Q5_d-X5FlxeeWcKxP_ilxqd5RmSBSg/edit?usp=sharing document for 2021]</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

<HR>
'''Thursday, January 14'''
<HR>
''Project presentation''
<DL>
<DT>9:00am-12:00pm</DT>
<DD>Project work/Prepare presentations for this afternoon</DD>
<DD>Please go to Discord for help, we will be available.</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>

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

<DT>1:00pm-2:00pm <DT>
<DD>Project Presentations (what you will do) /Project work</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>

<DT>2:00pm-4:00pm </DT>
<DD>Project work</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Friday, January 15'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Monday, January 18'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Tuesday, January 19'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Wednesday, January 20'''
<HR>
''Project work''
<DL>
<DT>9:00am-4:00pm</DT>
<DD>Project work</DD>

<DT>1:00pm-3:00pm</DT>
<DD>Project work/Office hours</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Thursday, January 21'''
<HR>
''Project Work & Poster Printing''
<DL>

<DD>Produce a PDF of your poster, presentation will online this year.</DD>
<DD>[http://teaching.healthtech.dtu.dk/material/22126/Posters.pdf Poster guide & requirements]</DD>

<DT>10:00am-12:00pm</DT>
<DD>Q&A: Practical information about the [http://teaching.healthtech.dtu.dk/material/22126/exam.pdf Exam]</DD>
<DD>Project work/Office hours</DD>
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Trine Zachariasen</DD>
</DL>

 

'''Friday, January 22'''
<HR>
''Poster session - Online''
<DL>
<DT>10:00am-2:00pm</DT>
<DD>Poster session part ('''exam''')</DD>
</DL>

Program 2021 - Revision history