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• 17:24, 19 March 2024 WikiSysop talk contribs created page Zip codes answers (Created page with " Please note that in UNIX, there is more than one way to do things. '''Q1:''' <pre> zcat /home/projects/22126_NGS/exercises/unix/ZIP_CODES.csv.gz |awk 'BEGIN{FS=","}{if($5=="\"NY\""){print $0}}'|wc -l </pre> <ol> <li><code>zcat</code>: Decompresses the ZIP_CODES.csv.gz file and outputs its content.</li> <li><code>awk 'BEGIN{FS=","}</code>: Sets the field separator to a comma for the CSV file.</li> <li><code>if($5=="\"NY\""){print $0}</code>: Checks if the 5th field (st...")
• 17:23, 19 March 2024 WikiSysop talk contribs created page Zip codes (Created page with " <H2>Extra fun with US zip codes</H2> <p>If you are 100% done with everything, you can have fun with the following exercise involving [https://en.wikipedia.org/wiki/ZIP_Code US zip codes]. This is mostly for people with previous Unix experience. </p> You will find the following file: <pre> /home/projects/22126_NGS/exercises/unix/ZIP_CODES.csv.gz </pre> No need to copy it or unzip it. You can view it with '''zcat''' or '''zless'''. csv stands for comma-separated val...")
• 17:23, 19 March 2024 WikiSysop talk contribs created page First look exercise answers (Created page with " <H2> Solutions </H2> Illumina data: 1. <pre> cd </pre> 2. <pre> mkdir first_look/ </pre> 3. <pre> cp /data/shared/exercises/first_look/reads.fastq.gz . </pre> 4. <pre> zless -S reads.fastq.gz </pre> 5. <pre> zcat /data/shared/exercises/first_look/reads.fastq.gz |wc -l </pre> 1000 lines so 1000/4 250 sequences. 1. <pre> tar xvfz /data/shared/exercises/first_look/pairedReads.tar.gz </pre> 2. <pre> head ERR243038_1.fastq ERR243038_2.fastq </pre>...")
• 17:22, 19 March 2024 WikiSysop talk contribs created page First look exercise (Created page with " <H2>Overview</H2> <p>In this exercise you will try to look at empirical NGS data. Additionally, you will try to use the '''screen''' command when using the shell. </p> <OL> <LI>Use standard UNIX commands to work with NGS data <LI>Use '''screen''' in shell </OL> <HR> <H2>First look at data</H2> <OL> <LI>Navigate to your home directory: <pre> cd </pre> '''cd''' without arguments will bring you back to your home directory. In our case, your home is: <pre> /home/people...")
• 17:18, 19 March 2024 WikiSysop talk contribs created page Unix answers (Created page with " 1. Use a text editor to (nedit/gedit/komodo/textwrangler) to create a file mycommands.txt where you write all commands and observations you do in the following exercises. Use copy/paste to copy the commands. Note: There are more standard text editors than nedit, etc. Examples are emacs, xemacs, vi, vim, and pico. Make sure that we can easily see which exercise you attempt to solve. 2. First list the files in the directory. <pre> ls </pre> 3. Copy ex1.acc to myfile.ac...")
• 17:14, 19 March 2024 WikiSysop talk contribs created page Logging on to pupil system (Created page with " <HR> <H2>Overview</H2> In this exercise, we will prepare our computers to log on to our servers called "pupilX", where X is 1/2/3. These are small but reliable machines. Please read the instructions carefully. Please be aware: there is '''no''' backup. All of your data will be deleted when the class concludes. <H2>Are you physically at DTU?</H2> First, make sure you are connected to the internet. If you are on campus, you do not need to do anything extra, however,...")
• 16:59, 19 March 2024 WikiSysop talk contribs created page Program 2024 (Created page with " '''REMEMBER TO BRING A LAPTOP FOR EXERCISES''' 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 and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your ful...")
• 16:54, 19 March 2024 WikiSysop talk contribs created page 22126 - Next Generation Sequencing Analysis (Created page with "<small>Introduction to Next-Generation Sequencing Analysis, 5 ECTS</small> <hr> <br> [http://kurser.dtu.dk/course/36626 DTU's Studies Handbook about #36626] [http://kurser.dtu.dk/course/36826 DTU's Studies Handbook about #36826]<be> Program 2024 Program 2023 Program 2022 Program 2021 Program 2020 Program 2019 The next course will be held in January 2024, the course runs every day for a three weeks period. The course consists of lectures, e...")
• 16:52, 19 March 2024 WikiSysop talk contribs created page MediaWiki:Mainpage (Created page with "22126 - Next Generation Sequencing Analysis")
• 16:51, 19 March 2024 WikiSysop talk contribs created page MediaWiki:Disclaimers (Created blank page)
• 16:51, 19 March 2024 WikiSysop talk contribs created page MediaWiki:Aboutsite (Created blank page)
• 16:50, 19 March 2024 WikiSysop talk contribs created page MediaWiki:Privacy (Created blank page)
• 16:48, 19 March 2024 MediaWiki default talk contribs created page Main Page