User contributions for WikiSysop

17:1017:10, 19 March 2024 diff hist +11,253‎ N 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..." current
17:0917:09, 19 March 2024 diff hist +2,502‎ N 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..." current
17:0917:09, 19 March 2024 diff hist +23,886‎ N 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..." current
17:0717:07, 19 March 2024 diff hist +11,508‎ N 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..." current
17:0617:06, 19 March 2024 diff hist +12,550‎ N Program 2021 ‎ 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..." current
17:0517:05, 19 March 2024 diff hist +1,343‎ N 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..." current
17:0517:05, 19 March 2024 diff hist +3,363‎ N 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..." current
17:0417:04, 19 March 2024 diff hist +4,574‎ N 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..." current
17:0317:03, 19 March 2024 diff hist +12,968‎ N 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..." current
17:0217:02, 19 March 2024 diff hist +12,699‎ N 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..." current
17:0117:01, 19 March 2024 diff hist +132‎ N MediaWiki:Sidebar ‎ Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22126/|Course 22126 * TOOLBOX" current
17:0017:00, 19 March 2024 diff hist +4,071‎ N 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>..." current
16:5916:59, 19 March 2024 diff hist −8‎ Cancerseq exercise ‎No edit summary current
16:5816:58, 19 March 2024 diff hist +9,763‎ N 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</..."
16:5616:56, 19 March 2024 diff hist +4,682‎ N 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..." current
16:5616:56, 19 March 2024 diff hist +15,177‎ N 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..." current
16:5416:54, 19 March 2024 diff hist 0‎ N File:Pca.png ‎No edit summary current
16:5416:54, 19 March 2024 diff hist 0‎ N File:Bc heatmap.png ‎No edit summary current
16:5316:53, 19 March 2024 diff hist 0‎ N File:Wilcoxon significant.png ‎No edit summary current
16:5316:53, 19 March 2024 diff hist 0‎ N File:Sample depth.png ‎No edit summary current
16:5316:53, 19 March 2024 diff hist +2,619‎ N 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)..." current
16:5216:52, 19 March 2024 diff hist 0‎ N File:Log fold diff sign.png ‎No edit summary current
16:5216:52, 19 March 2024 diff hist 0‎ N File:Bmi class.png ‎No edit summary current
16:5116:51, 19 March 2024 diff hist 0‎ N File:Comparing species abundance.png ‎No edit summary current
16:5116:51, 19 March 2024 diff hist 0‎ N File:Comparing shannon.png ‎No edit summary current
16:5016:50, 19 March 2024 diff hist 0‎ N File:Comparing richness.png ‎No edit summary current
16:5016:50, 19 March 2024 diff hist 0‎ N File:Downsized shannon.png ‎No edit summary current
16:4916:49, 19 March 2024 diff hist 0‎ N File:Downsized richness.png ‎No edit summary current
16:4816:48, 19 March 2024 diff hist 0‎ N File:Downsized sampledepth.png ‎No edit summary current
16:4816:48, 19 March 2024 diff hist 0‎ N File:Raw sampledepth.png ‎No edit summary current
16:4716:47, 19 March 2024 diff hist 0‎ N File:Raw richnessVSshannonZoom.png ‎No edit summary current
16:4716:47, 19 March 2024 diff hist 0‎ N File:Raw shannon.png ‎No edit summary current
16:4616:46, 19 March 2024 diff hist 0‎ N File:Raw richness.png ‎No edit summary current
16:4516:45, 19 March 2024 diff hist +10,393‎ N QuantitativeMetagenomics ‎ Created page with " <H3>Overview</H3> If you need to use metagenomics for your final project, we have a more thorough workflow that you will need to use https://teaching.healthtech.dtu.dk/22136/index.php/22136:Course_plan_autumn_2020 here. Since metagenomics data is often very large, it requires a lot of computational resources and time, we have cheated a little bit and prepared some data for you in advance! In this exercise we have done the assembly and counting across a cohort of..." current
16:4416:44, 19 March 2024 diff hist 0‎ N File:DDseq 350OTU.png ‎No edit summary current
16:4416:44, 19 March 2024 diff hist 0‎ N File:DDseq 100OTU.png ‎No edit summary current
16:4416:44, 19 March 2024 diff hist 0‎ N File:PrincipalComponents.png ‎No edit summary current
16:4316:43, 19 March 2024 diff hist 0‎ N File:Rawkaijubar.png ‎No edit summary current
16:4316:43, 19 March 2024 diff hist +3,019‎ N Kaiju solution ‎ Created page with "<b> Q1: What is nr_euk? And how do the choice of database influence the results of Kaiju?</b> nr stands for non-redundant and indicates, that each entry is only found once within the database. BLASTS' nr database contains bacteria, archea and fungi. euk indicates that microbial eukaryotes and fungi are included. The database should be intended as the target of the search, so it is of importance that it contains the organisms you are searching for. <b> Q2: Explain the..." current
16:4216:42, 19 March 2024 diff hist +21,585‎ N Kaiju exercise ‎ Created page with " ==Introduction== [http://kaiju.binf.ku.dk/ Kaiju] is a protein-based sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing or metatranscriptomics experiments. <br> Kaiju translates metagenomic sequencing reads into the six possible reading frames and searches for maximum exact matches (MEMs) of amino acid sequences in a given database of annotat..." current
16:4116:41, 19 March 2024 diff hist +2,972‎ N Longread exercise answers ‎ Created page with "'''Q1''' Counting all the lines minus the header gives us: <pre> zcat BGI_hg38_chr20.vcf.gz |grep -v "^#"|wc -l </pre> 1878 variants '''Q2''' We can try the following: <pre> zcat BGI_hg38_chr20.vcf.gz |grep -v "^#" |cut -f 10 |sed "s/:.*//g"|sort | uniq -c |sort -n </pre> <OL> <LI>grep -v "^#" grep -v: Inverts the match, i.e., selects lines that do not match the given pattern. "^#": The pattern to match lines starting with a hash (#). These lines are usually he..." current
16:4116:41, 19 March 2024 diff hist +7,233‎ N Longread exercise ‎ Created page with "<H2>Overview</H2> First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "longread" <LI>Navigate to the directory you just created. </OL> We will phase some variants using [https://www.biorxiv.org/content/10.1101/085050v2 WhatsHap] (no not the messaging app). First, what is phasing? Phasing means that we determine which base is on the same chromosome as another base for neighboring variants. Let's consider a small example with just two varia..." current
16:3916:39, 19 March 2024 diff hist 0‎ N File:Rnaseq fig3.png ‎No edit summary current
16:3916:39, 19 March 2024 diff hist 0‎ N File:Rnaseq fig2.png ‎No edit summary current
16:3916:39, 19 March 2024 diff hist 0‎ N File:Rnaseq fig1.png ‎No edit summary current
16:3716:37, 19 March 2024 diff hist +18,721‎ N Rnaseq exercise answers ‎ Created page with " <div class="page-content has-page-title"> <div id="overview-and-background" class="section level1"> <h1>Overview and background</h1> <div id="groups" class="section level2"> <h2>Groups</h2> <p>Please get into groups of 2-3. We don’t have enough computational power for all of you working alone. Please let the instructors know if you need help finding a group.</p> </div> <div id="assignment-notes" class="section level2"> <h2>Assignment notes</h2> <p>While some question..." current
16:3716:37, 19 March 2024 diff hist +11,080‎ N Rnaseq exercise ‎ Created page with " <div class="page-content has-page-title"> <div id="overview-and-background" class="section level1"> <h1>Overview and background</h1> <div id="groups" class="section level2"> <h2>Groups</h2> <p>Please get into groups of 2-3. We don’t have enough computational power for all of you working alone. Please let the instructors know if you need help finding a group.</p> </div> <div id="assignment-notes" class="section level2"> <h2>Assignment notes</h2> <p>While some question..." current
16:3616:36, 19 March 2024 diff hist +2,833‎ N Ancient DNA exercise answers ‎ Created page with "'''Q1''' the read length is about 100bp but the actual insert size is unknown. '''Q2''' very low, less than 1% '''Q3''' About 40bp. '''Q4''' About 25%. '''Q5''' As and Gs '''Q6''' The sample indeed looks ancient. If we did not see DNA fragmentation or damage it could be indicative of present-day human contamination. '''Q7''' <pre> wc -l world.fam wc -l world.bim </pre> 297 samples and 587772 SNPs. '''Q8''' <pre> cut -f2 world.sampleInfo.txt | tail -n +2..." current
16:3516:35, 19 March 2024 diff hist +11,971‎ N Ancient DNA exercise ‎ Created page with "<H2>Overview</H2> Adapted from Martin Sikora. First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "adna" <LI>Navigate to the directory you just created. </OL> We will try to # Authenticate ancient DNA # do some basic population genetics <h2> Data authentication</h2> Authentication involves making sure that the DNA that you have extracted from my fossil and sequenced is indeed from the fossil and not some modern contaminant. A big differe..." current
16:3516:35, 19 March 2024 diff hist +1,480‎ N Denovo solution ‎ Created page with "Q1. Illumina Q1A. discarded contains reads that are too short, pair1 and pair2 files contain the read pairs were both passed trimming and singleton are reads were one of the two pairs were discarded. Q2. Around 84 Q3. N = (M*L)/(L-K+1) = (84*99)/(99-15+1) = 97.84 Genome_size = T/N = (213721367+212523694)/97.84 = 4.35Mb Q4. Mean = 259 ; SD = 11 Q5. It is lower, this means that the actual kmer peak we found (unless you found one higher than 84) is higher (this would g..."

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19 March 2024

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