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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).
- 17:54, 19 March 2024 WikiSysop talk contribs uploaded File:Pca.png
- 17:54, 19 March 2024 WikiSysop talk contribs created page File:Bc heatmap.png
- 17:54, 19 March 2024 WikiSysop talk contribs uploaded File:Bc heatmap.png
- 17:53, 19 March 2024 WikiSysop talk contribs created page File:Wilcoxon significant.png
- 17:53, 19 March 2024 WikiSysop talk contribs uploaded File:Wilcoxon significant.png
- 17:53, 19 March 2024 WikiSysop talk contribs created page File:Sample depth.png
- 17:53, 19 March 2024 WikiSysop talk contribs uploaded File:Sample depth.png
- 17:53, 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)...")
- 17:52, 19 March 2024 WikiSysop talk contribs created page File:Log fold diff sign.png
- 17:52, 19 March 2024 WikiSysop talk contribs uploaded File:Log fold diff sign.png
- 17:52, 19 March 2024 WikiSysop talk contribs created page File:Bmi class.png
- 17:52, 19 March 2024 WikiSysop talk contribs uploaded File:Bmi class.png
- 17:51, 19 March 2024 WikiSysop talk contribs created page File:Comparing species abundance.png
- 17:51, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing species abundance.png
- 17:51, 19 March 2024 WikiSysop talk contribs created page File:Comparing shannon.png
- 17:51, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing shannon.png
- 17:50, 19 March 2024 WikiSysop talk contribs created page File:Comparing richness.png
- 17:50, 19 March 2024 WikiSysop talk contribs uploaded File:Comparing richness.png
- 17:50, 19 March 2024 WikiSysop talk contribs created page File:Downsized shannon.png
- 17:50, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized shannon.png
- 17:49, 19 March 2024 WikiSysop talk contribs created page File:Downsized richness.png
- 17:49, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized richness.png
- 17:48, 19 March 2024 WikiSysop talk contribs created page File:Downsized sampledepth.png
- 17:48, 19 March 2024 WikiSysop talk contribs uploaded File:Downsized sampledepth.png
- 17:48, 19 March 2024 WikiSysop talk contribs created page File:Raw sampledepth.png
- 17:48, 19 March 2024 WikiSysop talk contribs uploaded File:Raw sampledepth.png
- 17:47, 19 March 2024 WikiSysop talk contribs created page File:Raw richnessVSshannonZoom.png
- 17:47, 19 March 2024 WikiSysop talk contribs uploaded File:Raw richnessVSshannonZoom.png
- 17:47, 19 March 2024 WikiSysop talk contribs created page File:Raw shannon.png
- 17:47, 19 March 2024 WikiSysop talk contribs uploaded File:Raw shannon.png
- 17:46, 19 March 2024 WikiSysop talk contribs created page File:Raw richness.png
- 17:46, 19 March 2024 WikiSysop talk contribs uploaded File:Raw richness.png
- 17:45, 19 March 2024 WikiSysop talk contribs created page 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...")
- 17:44, 19 March 2024 WikiSysop talk contribs created page File:DDseq 350OTU.png
- 17:44, 19 March 2024 WikiSysop talk contribs uploaded File:DDseq 350OTU.png
- 17:44, 19 March 2024 WikiSysop talk contribs created page File:DDseq 100OTU.png
- 17:44, 19 March 2024 WikiSysop talk contribs uploaded File:DDseq 100OTU.png
- 17:44, 19 March 2024 WikiSysop talk contribs created page File:PrincipalComponents.png
- 17:44, 19 March 2024 WikiSysop talk contribs uploaded File:PrincipalComponents.png
- 17:43, 19 March 2024 WikiSysop talk contribs created page File:Rawkaijubar.png
- 17:43, 19 March 2024 WikiSysop talk contribs uploaded File:Rawkaijubar.png
- 17:43, 19 March 2024 WikiSysop talk contribs created page 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...")
- 17:42, 19 March 2024 WikiSysop talk contribs created page Kaiju exercise (Created page with "<!-- =22136 Metagenomics and Microbiome Analysis Kaiju exercise= --> ==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...")
- 17:41, 19 March 2024 WikiSysop talk contribs created page 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...")
- 17:41, 19 March 2024 WikiSysop talk contribs created page 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...")
- 17:39, 19 March 2024 WikiSysop talk contribs created page File:Rnaseq fig3.png
- 17:39, 19 March 2024 WikiSysop talk contribs uploaded File:Rnaseq fig3.png
- 17:39, 19 March 2024 WikiSysop talk contribs created page File:Rnaseq fig2.png
- 17:39, 19 March 2024 WikiSysop talk contribs uploaded File:Rnaseq fig2.png
- 17:39, 19 March 2024 WikiSysop talk contribs created page File:Rnaseq fig1.png
