4-8 April 2022 Data Carpentry (Genomics)

Wellcome Sanger Institute

Online

4-8 April 2022

1:00 pm - 5:00 pm BST

Instructors: Alison Meynert, Elton Rosas de Vasconcelos, Jannetta Steyn

Helpers: helper one, helper two

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: 4-8 April 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email hn7@sanger.ac.uk for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

Before starting Pre-workshop survey
1:00-3:00pm Project Organization and Management
3:00-3:30pm Break
3:30-5:00pm Introduction to the Command Line (Introducing the Shell, Navigating Files and Directories)

Day 2

1:00-3:00pm Introduction to the Command Line (Working with Files and Directories, Redirection)
3:00-3:30pm Break
3:30-5:00pm Introduction to the Command Line (Writing Scripts and Working with Data, Project Organization)

Day 3

1:00-3:00pm Data Wrangling and Processing for Genomics (Background and Metadata, Assessing Read Quality)
3:00-3:30pm Break
3:30-5:00pm Data Wrangling and Processing for Genomics (Trimming and Filtering)

Day 4

1:00-3:00pm Data Wrangling and Processing for Genomics (Variant Calling Workflow)
3:00-3:30pm Break
3:30-5:00pm Data Wrangling and Processing for Genomics (Automating a Variant Calling Workflow)

Setup

To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.