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  • Data Carpentry Virtual Workshop 2021

    4 March 2021

    Data Carpentry Virtual Workshop 2021 https://tess.elixir-europe.org/events/data-carpentry-virtual-workshop-2021 This hands-on workshop teaches fundamental data skills needed for anyone that deals with data and datasets. You will learn basic concepts, skills, and tools for working more effectively with data. The aim is to get researchers doing more in less time, and with less pain! We will cover: - data organisation in spreadsheets - data cleaning - SQL (Structured Query Language) - the command line - R for data analysis - visualisation using biological examples By the end of the workshop, learners should be able to more effectively manage and analyse data and apply the tools and approaches directly to their ongoing research. This four-day workshop will be delivered virtually, via Zoom, with input from 10:00-15:00 GMT, including breaks (see programme and further information tabs for more details). Who is this event for? Researchers in the life science and computational science disciplines. We particularly encourage PhD students and postdoctoral scientists to attend, but the course is open to everyone, at any stage of their career. The course is aimed at complete beginners; trainees are expected to have no prior knowledge of the tools or computational experience before attending. However, we will cover a lot of material and the training is quite fast paced, so be prepared to fully immerse yourself in the world of data management and analysis! Registration is currently reserved for certain groups. If you are interested in attending, please email training@earlham.ac.uk with a short expression of interest, explaining why you would like to attend the course. If places are available you will be provided with a password to complete the form. This training forms part of our BBSRC National Capability in Advanced Training 2021-03-04 09:00:00 UTC 2021-03-04 17:00:00 UTC Earlham Institute Earlham Institute training@earlham.ac.uk [] [] workshops_and_courses first_come_first_served []
  • Genome Annotation Workshop 2021

    15 April 2021

    Genome Annotation Workshop 2021 https://tess.elixir-europe.org/events/genome-annotation-workshop-2021 The value of a genome assembly depends heavily on the quality of its accompanying genome annotation. Automated procedures for annotation are therefore required that are robust to different genome characteristics and can efficiently and accurately annotate not only high-quality reference genomes but also large, fragmented “draft” genomes. The benefits of high-quality annotated genomes is well known - more accurate and complete annotation enables better interpretation of genome information within and across species, aiding researchers in their work to understand biological processes. Earlham Institute (EI) has developed a number of tools to support high quality annotation (including Mikado and Portcullis). Mikado (PMID: 30052957) is an open-source Python3 and Cython program that provides a framework for integrating transcripts from multiple sources into a consolidated set of gene annotations, while Portcullis (PMID: 30418570) is a tool to aid accurate splice junction detection. Both tools were utilised to aid the annotation of the wheat genome as part of the International wheat genome sequencing consortium (IWGSC, PMID: 30115783) and are being used to support EIs work in large collaborative genome sequencing projects such as the Wheat 10+ and Darwin Tree of Life In this 3-day virtual course, you will: - Get an overview of Next Generation Sequencing technologies relevant to genome annotation - Gain a deeper understanding of the benefits of each platform and have the confidence to select the right platform or combination of platforms for your project - Understand what to look for in a sample that will pass quality control and that will likely succeed in producing viable sequencing data, in particular expectations for pre-made libraries - Learn how to assess the quality of RNA-Seq data - Learn about de novo and reference guided transcriptome assembly and steps for processing long read data - Learn about alternative approaches for annotating protein coding genes in eukaryotic species - Hands on experience of annotation tools including tools and pipelines developed at the Earlham Institute. Who is this event for? Advanced PhD students and post-doctoral researchers who are undertaking projects involving annotating a genome assembly or generating transcriptome assemblies. Prerequisites You are expected to have experience with using the command line and will be looking to improve your awareness of different approaches and pipelines. This training forms part of our BBSRC National Capability in Advanced Training 2021-04-15 09:00:00 UTC 2021-04-15 17:00:00 UTC Earlham Institute Earlham Institute training@earlham.ac.uk [] [] workshops_and_courses registration_of_interest []

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