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- 08:37, 11 January 2026 Solution (hist | edit) [5,373 bytes] Mick (talk | contribs) (Created page with "<hr> <h2>Answers</h2> <p><b>Marsupials Newick</b></p> <pre> myTree <- read.tree(text = "((Echidna,Platypus),(American_Opossums,(Monito_del_Monte,((((Koalas,Wombats),(Possums,(Kangaroos,Wallabies))),(((Bandicoots,Bilby),Marsupial_Mole),((Tasmanian_Devil,Tasmanian_Tiger),Numbats)))))));") </pre> <p><b>Q1.</b> The two trees contain the same information about relationships, but the rooted tree additionally contains information about the most recent common ancestor of...")
- 11:12, 7 January 2026 Exercise and answers (hist | edit) [15,562 bytes] Mick (talk | contribs) (Created page with "<h2>Overview</h2> <p> In this mini-workshop you will familiarize yourself with <b>TADbit</b> (Serra et al., 2017): from FASTQ files to contact matrix and beyond. </p> <p> <b>A Primer into 3D Genomics: A Mini-Workshop</b><br> Juan Antonio Rodríguez, Globe Institute, University of Copenhagen<br> 9 January 2026, DTU </p> <hr> <h2>Outline of the exercises</h2> <ol> <li>Preprocess Hi-C FASTQ data</li> <li>Index reference genome</li> <li>Use TADbit to: <ol>...")
- 12:57, 6 January 2026 Microbial genomics exercise (hist | edit) [19,100 bytes] Rasmus (talk | contribs) (Created page with " Dear course participants, In this exercise you will analyse microbial genome sequences using bioinformatics tools that are commonly used for microbial diagnostics and research. == Background == We imagine that we are employed at a hospital to provide diagnostics for patient care. The laboratory has sequenced genomic DNA from a clinical specimen. The sequence reads are stored in FASTQ files that are compressed with gzip: * X * Y Use the following command to read t...")
- 14:19, 12 December 2025 Exercise (hist | edit) [11,942 bytes] Rasmus (talk | contribs) (Created page with "fefefeefefefefefe")
- 10:03, 20 November 2025 Advanced UNIX and Pipes (hist | edit) [5,871 bytes] Mick (talk | contribs) (Created page with "== Advanced UNIX and Pipes == This page covers standard input/output streams, redirection, pipes, file descriptors, and examples using Python scripts. These concepts are extremely useful in NGS analysis (e.g., chaining commands together, avoiding intermediate files, streaming FASTQ/BAM data, etc.). === stdout, stdin, stderr === Every UNIX command uses three data streams: * '''stdin''' (file descriptor 0) – input * '''stdout''' (file descriptor 1) – normal output...")
- 10:02, 20 November 2025 Basic UNIX notes (hist | edit) [3,758 bytes] Mick (talk | contribs) (Created page with "=== Introduction to UNIX === UNIX refers to a family of multitasking, multi-user operating systems that originated from AT&T Unix (Bell Labs, 1969). Many modern operating systems are UNIX-like and inherit its core principles of stability, flexibility, and powerful command-line tools. Although UNIX may appear complex at first, it is essential in bioinformatics and NGS analysis. Most tools you will use in this course (and in real research) run exclusively on the command l...")
- 15:43, 19 November 2025 Unix Exercises (hist | edit) [4,542 bytes] Mick (talk | contribs) (Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: None |Next: Python Recap and Objects |} You did complete the Course preparation, right? Otherwise, all of this will fail. == Required course material for the lesson == PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the updated PowerPoint. Video: [https:...")
- 09:23, 19 November 2025 Program 2026 (hist | edit) [12,091 bytes] Mick (talk | contribs) (Created page with " '''NOTE: THIS PAGE IS UNDER CONSTRUCTION WITH A NEW TEACHER IN 2026''' '''REMEMBER TO BRING A LAPTOP FOR EXERCISES''' Lectures will be in person in building [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23. <!-- 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. --> The course has two main parts, the...")