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Research Environment Training Sessions: What tools and workflows should I use to fulfil an overall goal?

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Research Environment Training Sessions: What tools and workflows should I use to fulfil an overall goal?

It can be hard to get started with a research project in the Research Environment (RE), with an abundance of data and tools available. In this training session we will look at some of the major use-cases in research and the steps involved in carrying these out, both at a large and small scale. Instead of going into deep detail on these paths, we will point you to tutorials and documentation to get you going with the different steps of the process.

The use cases we’ll be looking at are:

  • I'm interested in a phenotype and I want to know what variants are related
  • I'm interested in a gene and I want to know what phenotypes are related
  • I want to know more about pathogenicity of different variant types on a large scale
  • I want to find a diagnosis for patients who didn't get one through primary clinical interpretation

For many of these use-cases, we will point you towards resources to carry out these projects at a large scale, using programmatic and command-line resources, and at a small scale using point-and-click tools. Bear in mind that is not always feasible to do this kind of research at both scales.

You are only allowed to attend this session if you are eligible for data access. This means that you are a GECIP or Discovery Forum member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criterion by 13 November 2023, you will be unregistered for this session.

You can find materials from past training sessions and information on upcoming training sessions on the Genomics England Research Environment User Guide.


Agenda

13.30 Introduction and admin

13.35 Identifying variants associated with a phenotype

13.50 Identifying phenotypes associated with a gene

14.05 Studying pathogenicity of variant types at scale

14.20 Finding diagnoses for patients who didn’t get one through primary clinical interpretation

14.35 Getting help and questions



Learning objectives

After this training you will know:

  • the main steps involved in common use-cases in the RE
  • how to access training materials and navigate the documentation


Target audience

This training is aimed at researchers:

  • working with the Genomics England Research Environment
  • who are looking for a start point for their research project goals
  • either programmers or non-programmers

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