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A Genomics Data Carpentry Workshop

105 Cargill Building, University of Minnesota

Nov 21-22, 2016

9:00 am - 4:30 pm

Instructors: Jon Badalamenti, Tracy Teal

Helpers: Titus Brown, Lauren Mills

General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover metadata organization in spreadsheets, data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.

Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The course is aimed at graduate students and other researchers.

Where: 1500 Gortner Avenue, St. Paul, MN 55108. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Preliminary Schedule


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

Pre-workshop Survey

Post-workshop Survey

Workshop overview

Day 1

Module 1: Workshop Introduction Module 2 Data tidiness
  • Think about and understand the types of data and metadata a sequencing experiment will generate
  • Gain a general understanding of data organization
Module 3: Using cloud computing for genomics
  • understand what cloud computing is and why it's useful
  • log in to remote computing resources
Module 4: Introduction to the command line
  • learn to navigate at the command line
  • search files

Day 2

Module 5: Data wrangling and processing Minnesota Supercomputing Institute introduction Modules for future reference:
Variant Calling Workflow or R for data analysis and visualization


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

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.