All public logs

Combined display of all available logs of 22126. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 16:28, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 2 answers (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
• 16:27, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 1 answers (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
• 17:20, 10 December 2024 Gabre talk contribs created page Unix pipes (Created page with "Welcome! This small guide contains a lot of information and examples that will help you as you start learning Linux. In addition to simple Linux commands, this tutorial also provides three Python scripts, that you can run and try out the concepts yourself. # Basic Unix Commands and Concepts This is where your journey begins! If you are new to Unix-based systems and also got used to Windows or MacOS, you really need a brief explanation of a few key commands and concept...")
• 15:06, 29 November 2024 Gabre talk contribs created page SNP calling exercise part 2 (Created page with " <H2> Filtering</H2> We saw that the data contains some calls of poor quality. Ideally, we do not want to carry over these calls into downstream analyses. We will explore how to filter out genotype data. <H3> Hard filtering </H3> A major downside of soft filtering is that does not apply for samples for which we do not have a good representation of the genetic diversity. An alternative is to do hard filtering meaning filtering the variants according to predetermined...")
• 14:35, 29 November 2024 Gabre talk contribs created page SNP calling exercise answers part 1 (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
• 14:33, 29 November 2024 Gabre talk contribs created page SNP calling exercise part 1 (Created page with "<H2>Overview</H2> First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "variant_call" <LI>Navigate to the directory you just created. </OL> We will: <OL> <LI>Genotype some whole-genome sequencing data. <LI>Get acquainted with VCF files <LI>Soft filtering <LI>Hard filtering <LI> Annotation of variants </OL> ---- <H2>Genotyping</H2> We will genotype a chromosome from a BAM file that has been processed using the steps we detailed before. It i...")
• 15:40, 14 November 2024 Gabre talk contribs created page Unix notes (Created page with "Certainly! Here's a Markdown version of the UNIX instructions from the provided PDF: # Using UNIX UNIX primarily operates through a command-line interface, allowing users to execute commands directly. While this may initially seem less intuitive than graphical interfaces, its power becomes evident with experience. ## Obtaining UNIX There are various methods to access UNIX: - **Windows**: Download and install [MobaXTerm](https://mobaxterm.mobatek.net/). - **Mac**: ma...")
• 14:29, 7 November 2024 Gabre talk contribs created page Program 2025 (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...")
• 16:21, 4 November 2024 User account Gabre talk contribs was created by WikiSysop talk contribs
• 17:10, 19 March 2024 WikiSysop talk contribs created page Program 2019 (Created page with "'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, '''Building 208, Room 062''' in Lyngby ([https://www.google.com/maps/place/DTU+bygning+208%2F+DTU+Building+208/@55.7863894,12.520095,357m/data=!3m1!1e3!4m5!3m4!1s0x46524e62f280d429:0x1bbb0474519984b5!8m2!3d55.787537!4d12.5182208 map]). The courses has two main parts, the first half is lectures and exerc...")
• 17:09, 19 March 2024 WikiSysop talk contribs created page Metagenomic assembly solution (Created page with "Q1. We cant really find the bell shaped distributions in our samples - except for in MH0032 where there are two very small bell shaped coverage distributions. Q2. This is because we have many organisms with relative low abundance. This makes it very hard to distinguish them using coverage information. Q3. It will probably perform much like SOAPdenovo. Q4. There arent really any major differences in the coverage distributions between the assemblers, the metagenome asse...")
• 17:09, 19 March 2024 WikiSysop talk contribs created page Metagenomic assembly exercise (Created page with "<H2>Overview</H2> <p>In this exercise we will try <i>de novo</i> assemble a metagenomic dataset of Illumina paired end reads from a stool sample. The data is part of the MetaHit project and was published [http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html here]. These are just two samples of 396, in the next exercise (tomorrow) you will analyze data from 124 samples. Today, you will try to: <OL> <LI>Analyze k-mer distributions <LI>Assemble using SOA...")
• 17:07, 19 March 2024 WikiSysop talk contribs created page Program 2020 (Created page with " '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, '''Building 210, Room H162''' in Lyngby ([https://goo.gl/maps/hyifvFrZ5cPLroCv8 map]). The courses 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. This term we will be using Piazza for class discussion. The...")
• 17:06, 19 March 2024 WikiSysop talk contribs created page Program 2021 (Created page with " <!--- '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' --> 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...")
• 17:05, 19 March 2024 WikiSysop talk contribs created page CfDNA exercise answers (Created page with "'''Q1''' Using: <pre> samtools stat /data/shared/exercises/cfdna/patient_1.bam > patient1.stat samtools stat /data/shared/exercises/cfdna/patient_2.bam > patient2.stat plot-bamstats -p patient1 patient1.stat plot-bamstats -p patient2 patient2.stat firefox patient1.stat firefox patient2.stat </pre> Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2. '''Q2''' We first run: <p...")
• 17:05, 19 March 2024 WikiSysop talk contribs created page CfDNA exercise (Created page with "<H2>Overview</H2> First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "cfdna" <LI>Navigate to the directory you just created. </OL> Blood was drawn from 2 patients. One of those is a healthy patient, the other one has lung squamous cell carcinoma. It was previously [https://www.cell.com/fulltext/S0092-8674(15)01569-X reported] that tumors can leave a signature in the blood plasma via cell-free DNA, namely: # The distribution of fragment l...")
• 17:04, 19 March 2024 WikiSysop talk contribs created page Logging on to Cloud system (Created page with " <HR> <H2>Overview</H2> In this exercise, we will prepare our computers to log on to our very own cloud system on Computerome. This is done via a Virtual Private Network (VPN). <HR> <H3>Student accounts</H3> <p>To be able to perform the exercises and project you will need an account to log in to the cloud computers. Open the [https://docs.google.com/spreadsheets/d/1TAj59JQurp6ene6kOlrug9mRJSHpdsIS8U6KKvkcLN0/edit?usp=sharing google doc], find student id and determin...")
• 17:03, 19 March 2024 WikiSysop talk contribs created page Program 2022 (Created page with " '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' 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 first half is lectures and exercises and the last half is project work ending with the exam on '''Friday 21st of January'''. <!-- This term, we will be using Piazza for class disc...")
• 17:02, 19 March 2024 WikiSysop talk contribs created page Program 2023 (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...")
• 17:01, 19 March 2024 WikiSysop talk contribs created page MediaWiki:Sidebar (Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22126/|Course 22126 * TOOLBOX")
• 17:00, 19 March 2024 WikiSysop talk contribs created page Cancerseq exercise answers (Created page with "'''Q1''' We run: <pre> gatk Mutect2 -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/cancer_seq/TCRBOA2-N-WEX_recaled.bam -I /home/projects/22126_NGS/exercises/cancer_seq/TCRBOA2-T-WEX_recaled.bam -normal TCRBOA2-N-WEX -L chr10:3100000-5100000 --germline-resource /home/databases/databases/GRCh38/somatic-hg38_af-only-gnomad.hg38.vcf.gz -O TCRBOA2.vcf.gz </pre> Then either: <pre>...")
• 16:58, 19 March 2024 WikiSysop talk contribs created page Cancerseq exercise (Created page with " <H2>Overview</H2> Adapted from an original exercise by Marcin Krzystanek and Aron Eklund. First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "cancerseq" <LI>Navigate to the directory you just created. </OL> In this exercise, we learn the differences between standard genotyping and genotyping for cancer-seq: <OL> <LI>Somatic mutation calling <LI>Interpretation of the resulting somatic mutations </OL> <H2>Somatic mutation calling</...")
• 16:56, 19 March 2024 WikiSysop talk contribs created page Genomic epidemiology solution (Created page with "Q1. We can use the fastx tools to get this information <pre> fastx_readlength.py --i reads_R1.fastq.gz --gz fastx_readlength.py --i reads_R2.fastq.gz --gz </pre> This should give you the answer. Reads: 2*1408847 = 2,817,694; Bases: 284587094 Task1 - can be accomplished using a quality control tool like fastqc. <pre> mkdir fastqc fastqc -o fastqc reads_R*.fastq.gz firefox fastqc/reads_R1_fastqc.html fastqc/reads_R2_fastqc.html & </pre> Q2. There are no overrepresented...")
• 16:56, 19 March 2024 WikiSysop talk contribs created page Genomic epidemiology exercise (Created page with "<H3>Overview</H3> You are a bioinformatician working with epidemiology in Copenhagen. In the last couple of days more and more people have been admitted to the Hospitals in the region with severe bacteremia (bacteria in the bloodstream) and several patients, especially infants and young children, have had fatal outcomes. Luckily the probable causative infectious bacteria has been isolated and sequenced on a desktop sequencer and now it is your job to find out: <OL> <LI...")
• 16:54, 19 March 2024 WikiSysop talk contribs created page File:Pca.png
• 16:54, 19 March 2024 WikiSysop talk contribs uploaded File:Pca.png
• 16:54, 19 March 2024 WikiSysop talk contribs created page File:Bc heatmap.png
• 16:54, 19 March 2024 WikiSysop talk contribs uploaded File:Bc heatmap.png
• 16:53, 19 March 2024 WikiSysop talk contribs created page File:Wilcoxon significant.png
• 16:53, 19 March 2024 WikiSysop talk contribs uploaded File:Wilcoxon significant.png
• 16:53, 19 March 2024 WikiSysop talk contribs created page File:Sample depth.png
• 16:53, 19 March 2024 WikiSysop talk contribs uploaded File:Sample depth.png
• 16:53, 19 March 2024 WikiSysop talk contribs created page QuantitativeMetagenomicsSolution (Created page with "'''Q1. How many samples do we have and how many genes?''' <pre>> str(Counts) int [1:251436, 1:401] </pre> 251436 genes and 401 individuals '''Q2. What's the sample depth range?''' <pre>> range(sampleDepth) [1] 1533776 41391478 </pre> 1533776 to 41391478 File:Sample_depth.png The figure shows the number of samples (persons) on the y-axis containing the displayed number of reads on the x-axis '''Q3. How many species are there in total?''' <pre> str(taxCounts)...")
• 16:52, 19 March 2024 WikiSysop talk contribs created page File:Log fold diff sign.png
• 16:52, 19 March 2024 WikiSysop talk contribs uploaded File:Log fold diff sign.png
• 16:52, 19 March 2024 WikiSysop talk contribs created page File:Bmi class.png
• 16:52, 19 March 2024 WikiSysop talk contribs uploaded File:Bmi class.png
• 16:51, 19 March 2024 WikiSysop talk contribs created page File:Comparing species abundance.png
• 16:51, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing species abundance.png
• 16:51, 19 March 2024 WikiSysop talk contribs created page File:Comparing shannon.png
• 16:51, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing shannon.png
• 16:50, 19 March 2024 WikiSysop talk contribs created page File:Comparing richness.png
• 16:50, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing richness.png
• 16:50, 19 March 2024 WikiSysop talk contribs created page File:Downsized shannon.png
• 16:50, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized shannon.png
• 16:49, 19 March 2024 WikiSysop talk contribs created page File:Downsized richness.png
• 16:49, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized richness.png
• 16:48, 19 March 2024 WikiSysop talk contribs created page File:Downsized sampledepth.png
• 16:48, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized sampledepth.png
• 16:48, 19 March 2024 WikiSysop talk contribs created page File:Raw sampledepth.png