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  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 3

    27 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 3 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-3 ### Genotype calling from Illumina files The third of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce genotyping SNP array chips with particular emphasis on the H3Africa genotype chip. The lecture will cover common file formats when obtaining genotyping chip data from a service provider such as Illumina and software used for genotype calling. This lecture will also cover genotype calling, sample and probe quality control, probe viewing and exporting of data using GenomeStudio. Converting the data to PLINK format and some tips on troubleshooting and common pitfalls will be discussed. 2018-08-27 15:00:00 UTC 2018-08-27 16:00:00 UTC H3ABioNet Population genomics Bioinformatics Genotyping experiment Genomics Computational biology H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genotype callingH3ABioNetGenotype callingGenome StudioH3Africa genotyping arrayAfrican populationsArray processingIllumina arraysFile formatsAnnotationsNon-polymorphicTop/Bottom annotationGenotype array probesIntensitiesConvert to PLINK format BioinformaticsGenome Wide Association Studies
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4

    29 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-4 ### Quality control and its importance in GWAS In the fourth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS), the importance of doing good quality control for a GWAS will be discussed. The lecture will cover the types of errors one should control for, the specific bioinformatics tools used for quality control. Specific sample and SNP quality control steps that should be undertaken in a GWAS will be explored using specific examples. 2018-08-29 15:00:00 UTC 2018-08-29 16:30:00 UTC H3ABioNet Genotyping experiment GWAS study Computational biology Bioinformatics Population genomics Population genetics H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genome Wide Association StudiesGenotype callingH3Africa genotyping arrayAfrican populationsQuality Control for GWASSample Quality ControlSNP Quality ControlPopulation GenomicsGenotypingPLINK formatPrincipal Component AnalysisLow minor allele frequencyMissingnessGWAS workflowDiscordant Sex informationNextflowGenotyping rate callHeterozygosity rateRelated and duplicate individualsIdentity by DescentHardy Weinberg EquilibriumBioinformaticsH3ABioNet GWAS 2018 Lecture Series
  • A short tour of UCSC data

    24 October 2018

    A short tour of UCSC data https://tess.elixir-europe.org/events/a-short-tour-of-ucsc-data 2018-10-24 11:00:00 UTC 2018-10-24 12:30:00 UTC ARDC Australia, Australia Australia Australia Genomics Bioinformatics [] [] [] [] [] genome browsingBioinformatics
  • Metagenomics Analysis using Galaxy

    11 August 2020

    Metagenomics Analysis using Galaxy https://tess.elixir-europe.org/events/genome-assembly-using-galaxy-bfd44b56-d4a3-4863-a62b-e7656374a9a9 This workshop will cover the concepts of 16S bacterial metagenomics analysis. You will learn about pre-processing and quality -filtering of your data, assembly of reads into Operational Taxonomic Units (OTUs), and visualisation and export of data for further analysis. 2020-08-11 09:00:00 UTC 2020-08-11 17:00:00 UTC QCIF Online workshop delivered via Zoom, N/A, Australia Online workshop delivered via Zoom N/A Queensland Australia N/A QCIF Mark Crowe - mark.crowe@qcif.edu.au [] Postgraduate studentsPostdoctoral researchers workshops_and_courses first_come_first_served MetagenomicsGalaxyBioinformatics
  • UK Conference of Bioinformatics and Computational Biology 2020

    29 - 30 September 2020

    UK Conference of Bioinformatics and Computational Biology 2020 https://tess.elixir-europe.org/events/uk-conference-of-bioinformatics-and-computational-biology-2020 The UK-CBCB conference is designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. The conference will be applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources. 2020-09-29 09:00:00 UTC 2020-09-30 17:00:00 UTC Earlham Institute Data management Bioinformatics Metabolomics Earlham Institute Training@earlham.ac.uk [] [] meetings_and_conferences registration_of_interest Bioinformaticslife sciencesMetabolomicsSingle Cell GenomicsMicrobial evolution
  • ELIXIR CZ Friday Coffee 2021 - 3DPatch : Structure visualization with residue conservation

    12 February 2021

    Elixir node event
    ELIXIR CZ Friday Coffee 2021 - 3DPatch : Structure visualization with residue conservation https://tess.elixir-europe.org/events/elixir-cz-friday-coffee-2021-3dpatch-structure-visualization-with-residue-conservation 2021-02-12 09:30:00 UTC 2021-02-12 10:30:00 UTC ELIXIR-CZ [] [] [] [] [] Bioinformaticsstructural biology
  • Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R

    15 February - 8 March 2021

    Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R https://tess.elixir-europe.org/events/new-course-bioinformatics-for-biologists-an-introduction-to-linux-bash-scripting-and-r # Overview ### Duration: 2 weeks, 5 hours per week **Free Certificate of Achievement available** on satisfactory completion ### Start Date: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join this course? Bioinformatics is a rapidly growing academic field, and one that promises to change how we analyse and compare biological data. On this course, you’ll get familiar with Linux – the operating system often used to access and analyse biological data. You’ll come away able to navigate it using the command line, understanding how to write scripts and prepare data files for further analysis and visualisation. ### Who is this course for? This course will appeal to students, biologists, and research scientists with an interest in bioinformatics. Learners are expected to have some knowledge of or experience with life sciences, but no prior knowledge of computing or bioinformatics is expected. There are no formal prerequisites. # Programme ### Course start dates This course will be repeated twice a year. ### What topics will you cover? * What is Linux? Why Linux for biologists? * The Linux file system and navigating around it via the command line * Manipulation and searching of data files using the command line to access useful biological data * The basics of writing Bash scripts and its use for process automation * Guidelines and recommendations for best practice preparation of data files under Linux for exporting to other environments (use of R for further analysis and visualisation) * Exercises on biological data using different case scenarios ### What will you achieve? By the end of the course, you‘ll be able to... * identify main characteristics of Linux and its use in biology * describe the structure of a Linux file system * use Linux commands to navigate the file system * perform Linux commands to manipulate and interrogate biological data files * prepare biological data files under Linux for exporting into other environments such as R * write and execute simple shell scripts in order to automate processing of data # Educators ## Lead Educators ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Fatma Guerfali Researcher at Institut Pasteur in Tunis and Trainer in Bioinformatics. Passionate about data analysis and visualization for pathogens related Genomics and Transcriptomics ### Victoria Offord As a Prinicipal Bioinformatician in Experimental Cancer Genetics at the Wellcome Sanger Institute, I develop and run pipelines for saturation mutagenesis, CRISPR screens, RNA-Seq and variant calling. ### Mark Sheppard I am the Assistant IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests include machine learning and coding. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible 2021-02-15 09:00:00 UTC 2021-03-08 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] entermostrelevantkeywordhereHDRUK

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