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WikiSysop: Created page with "'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 303A] in auditorium 45. Offline discussions will take place on Discord (https://discord.gg/4yVB6vMG2n). Please register with your '''full name'''. Will use Discord for online classes and collaboration with your project partners. <!-- Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with..."
2024-03-19T16:02:53Z
<p>Created page with "'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 303A] in auditorium 45. Offline discussions will take place on Discord (https://discord.gg/4yVB6vMG2n). Please register with your '''full name'''. Will use Discord for online classes and collaboration with your project partners. <!-- Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with..."</p>
<p><b>New page</b></p><div>'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES'''<br />
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Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 303A] in auditorium 45. Offline discussions will take place on Discord (https://discord.gg/4yVB6vMG2n). Please register with your '''full name'''. Will use Discord for online classes and collaboration with your project partners.<br />
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<!--<br />
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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.<br />
--><br />
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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 20th of January 2023'''.<br />
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<!--<br />
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]<br />
--><br />
<br />
=== Course Program - January 2023 ===<br />
<br />
<br />
<HR><br />
'''Monday, January 2'''<br />
<HR><br />
''Introduction - Next Generation Sequencing''<br />
<DL><br />
<DT>9:00am-9:30am</DT> <br />
<DD>Introduction to course <br />
([https://teaching.healthtech.dtu.dk/material/22126/2023/11_Introduction_to_course_GR.pdf Lecture slides])<br />
</DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>9:30am-10:00am</DT><br />
<dd>Introduction to NGS <br />
([https://teaching.healthtech.dtu.dk/material/22126/2023/12_Introduction_to_NGS_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:00am-10:45am</DT><br />
<DD>2nd and 3rd generation NGS Technologies <br />
([https://teaching.healthtech.dtu.dk/material/22126/2023/13_Introduction_to_NGS_technology_GR.pdf Lecture slides])</DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:45am-11:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>11:00am-12:00pm</DT><br />
<DD>Tech talk group formation and group work <br />
([https://teaching.healthtech.dtu.dk/material/22126/2023/14_Tech_Talks_GR.pdf Lecture slides])<br />
([https://docs.google.com/spreadsheets/d/1-Add0-Zw1JvUaoPYMmHuxlkPxnF49jSffFZ6L2ajL4I/edit?usp=sharing Student Groups 2023]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>12:00pm-1:00pm</DT> <br />
<DD>''Lunch Break''</DD><br />
<br />
<DT>1:00pm-1:30pm</DT><br />
<DD>Exercise: Logging on to our pupil servers ([[Logging on to pupil system]])</DD><br />
<DD>Peter Wad Sackett, Nicola Vogel, Louis Kraft, Gabriel Renaud </DD><br />
<br />
<DT>1:30pm-2:15pm </DT><br />
<DD>Introduction to UNIX <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."]) <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]]) <br />
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD><br />
<DD>Peter Wad Sackett, Nicola Vogel, Louis Kraft </DD><br />
<br />
<DT>2:15pm-2:30pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:30pm-3:30pm </DT><br />
<DD>Introduction to UNIX (continued)<br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."]) <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]])<br />
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD><br />
<DD>Peter Wad Sackett, Nicola Vogel, Louis Kraft </DD><br />
<br />
<DT>3:30pm-4:00pm </DT><br />
<DD>First look at data<br />
([[First look exercise]])<br />
<DD>Peter Wad Sackett, Nicola Vogel, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Tueday, January 3'''<br />
<HR><br />
''Data pre-processing & Alignment''<br />
<br />
<DL><br />
<DT>9:00am-10:45am </DT><br />
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2023/21_Data_Basics_GR.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD><br />
<DD>Gabriel Renaud, Nicola Vogel, Louis Kraft</DD><br />
<br />
<br />
<DT>10:45am-11:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>11:00am-12:00pm </DT><br />
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2023/22_Data_Preprocessing_GR.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD><br />
<DD>Gabriel Renaud </DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-2:15pm</DT><br />
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2023/23_Alignment_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud </DD><br />
<br />
<DT>2:15pm-2:30pm</DT><br />
<DD>''Break'' </DD><br />
<br />
<br />
<DT>2:30pm-2:45pm</DT><br />
<DD>Brief reminder on probabilities and Bayesian theory ([https://teaching.healthtech.dtu.dk/material/22126/2023/24_Bayesian_reminder_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>2:45pm-4:00pm</DT><br />
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD><br />
<DD>Gabriel Renaud, Nicola Vogel, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Wednesday, January 4'''<br />
<HR><br />
<br />
''Alignment & Genotyping''<br />
<DL><br />
<DT>9:00am-9:30am</DT><br />
<DD>Functional Human Variation</DD><br />
<DD>Gabriel Renaud, ([https://teaching.healthtech.dtu.dk/material/22126/2023/41_Functional_Human_Variation_GR.pdf Lecture slides])</DD><br />
<br />
<DT>9:30am-10:15am</DT><br />
<DD>Alignment postprocessing & variant calling ([https://teaching.healthtech.dtu.dk/material/22126/2023/42_post_alignment_variantcalling_GR.pdf Lecture slides])</DD><br />
<br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:15am-10:30am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:30am-12:00pm</DT><br />
<DD>Exercise: Postprocessing & variant calling ([[Postprocess exercise]]) ([[Postprocess_exercise_answers]]) ([[SNP calling exercise]]) ([[SNP_calling_exercise_answers]])</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft </DD><br />
<br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-1:45pm </DT><br />
<DD>Lecture: de novo assembly ([https://teaching.healthtech.dtu.dk/material/22126/2023/43_de_novo_assembly_course_GR.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Thursday, January 5'''<br />
<HR><br />
''Metagenomics''<br />
<DL><br />
<DT>9:00am-9:45am </DT><br />
<DD>Metagenomics & Binning ([https://teaching.healthtech.dtu.dk/material/22126/2023/Metagenomics_binning.pdf Lecture slides])</DD><br />
<DD>Asker Brejnrod</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Exercise: Kaiju: Taxonomic classification ([[Kaiju exercise]]) ([[Kaiju solution]]) </DD><br />
<DD>Asker Brejnrod,Louis Kraft</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-1:45pm</DT><br />
<DD>Lecture: Quantitative Metagenomics ([https://teaching.healthtech.dtu.dk/material/22126/2023/Quantitative_metagenomics.pdf Lecture slides])</DD><br />
<DD>Asker Brejnrod</DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Exercise: Quantitative Metagenomics ([[QuantitativeMetagenomics]]) ([[QuantitativeMetagenomicsSolution]]) </DD><br />
<DD>Asker Brejnrod, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Friday, January 6'''<br />
<HR><br />
''Long read tech and recap test''<br />
<DL><br />
<DT>9:00am-9:45am </DT><br />
<DD>Lecture: Long read sequencing ([https://teaching.healthtech.dtu.dk/material/22126/2021/cfDNA_lecture_2020_SB.pdf Lecture slides])</DD><br />
<DD>Shilpa Garg</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00am</DT><br />
<DD>Exercise: Long read technology ([[longread exercise]])([[longread_exercise_answers]])</DD><br />
<DD>Shilpa Garg, Josh Rubin, Louis Kraft</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-1:45pm</DT><br />
<DD>Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2023/test_2023.pdf Test 2023])([https://teaching.healthtech.dtu.dk/material/22126/2023/test_2023_withA.pdf answers])</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft </DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Time to work on this week's exercises</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<br />
<HR><br />
'''Monday, January 9'''<br />
<HR><br />
<br />
''RNA-seq and Ancient DNA''<br />
<DL><br />
<br />
<DT>9:00am-9:45am</DT><br />
<DD>Lecture: RNAseq ([https://teaching.healthtech.dtu.dk/material/22126/2023/ngs_transcriptomics_kvs_2023_without_solutions_v2.pdf Lecture slides])</DD><br />
<DD>Kristoffer Vitting-Seerup</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Exercise: RNAseq ([shorturl.at/nzBPQ Rnaseq_exercise]) ([[Rnaseq_exercise_answers]]) </DD><br />
<DD>Kristoffer Vitting-Seerup, Josh Rubin, Louis Kraft </DD><br />
<br />
<DT>12:00pm-1:00pm</DT> <br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DL><br />
<DT>1:00pm-2:00pm</DT><br />
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2021/dtu_adna_2021.pdf Lecture slides])</DD><br />
<DD>Martin Sikora</DD><br />
<br />
<DT>2:00pm-2:15pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:15pm-4:00pm</DT><br />
<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD><br />
<DD>Martin Sikora, Josh Rubin, Louis Kraft</DD><br />
<br />
<br />
<BR><br />
<br />
<HR><br />
'''Tuesday, January 10'''<br />
<HR><br />
<br />
''Genomic Epidemiology and tech talk''<br />
<br />
<DL><br />
<DT>9:00am-9:55am</DT><br />
<DD>Exercise: Genomic Epidemiology ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>9:55am-10:10am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:10am-12:00pm</DT> <br />
<DD>Case story: Genomic Epidemiology ([https://teaching.healthtech.dtu.dk/material/22126/2023/Genomic_epidemiology_NGScourse_Jan2023.pdf Lecture])</DD><br />
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-2:00pm </DT><br />
<DD>Tech talk work</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft </DD><br />
<br />
<DT>2:00pm-4:00pm </DT><br />
<DD>TechTalks Presentations</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft </DD><br />
<br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Wednesday, January 11'''<br />
<HR><br />
''CancerSeq & Project work''<br />
<br />
<DT>9:00am-9:45am </DT><br />
<DD>Lecture: Cancer-seq ([https://teaching.healthtech.dtu.dk/material/22126/2023/Cancer_Genomics_EP_2023_2.pdf Lecture slides]) </DD> <br />
<DD>Elena Papaleo </DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD><br />
<DD>Adrian Otamendi, Josh Rubin, Louis Kraft </DD><br />
</DL><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-1:45pm </DT> <br />
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2023/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/2023/posters.tar.gz Examples from previous courses]) </DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
<br />
<DT>1:45pm-4:00pm </DT> <br />
<DD>Projects & Group formation, prepare an outline for tomorrow. please write group names in the [https://docs.google.com/document/d/1Flu6t3RRm44ExyGli6X_yOqoaK1_02yWZiOWeIPlgSc/edit?usp=sharing document for 2023]</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<br />
<BR><br />
<br />
<HR><br />
'''Thursday, January 12'''<br />
<HR><br />
''Project presentation''<br />
<DL><br />
<DT>9:00am-12:00pm</DT> <br />
<DD>Project work/Prepare your project outline for this afternoon</DD><br />
<!--<br />
<DD>Please go to Discord for help, we will be available.</DD><br />
--><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break''</DD><br />
<br />
<DT>1:00pm-2:00pm <DT><br />
<DD>Project outlines (what you will do) /Project work</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
<br />
<DT>2:00pm-4:00pm </DT><br />
<DD>Project work</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Friday, January 13'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Monday, January 16'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Tuesday, January 17'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Wednesday, January 18'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Thursday, January 19'''<br />
<HR><br />
''Project Work & Poster Printing''<br />
<DL><br />
<br />
<DD>Please print your poster.</DD><br />
<DD>[http://teaching.healthtech.dtu.dk/material/22126/Posters.pdf Poster guide & requirements]</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Q&A: Practical information about the exam</DD><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Louis Kraft</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Friday, January 20'''<br />
<HR><br />
''Poster session''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Poster session part ('''exam''')</DD><br />
</DL></div>
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