June 5-6, 2018
9:00 am - 4:30 pm
Instructors: Upendra Kumar Devisetty, Elijah Lowe
Helpers: Nick Krom, Liang Sun, Andrew Bancroft, Zach Robinson
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 workshop is open to all Noble Research Institute researchers that want to learn the basics of working with genomic data. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Kruse Auditorium, 2510 Sam Noble Parkway, Ardmore, Oklahoma. Get directions with OpenStreetMap or Google Maps.
When: June 5-6, 2018. Add to your Google Calendar.
Requirements: Participants must bring a laptop 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). They are also required to abide by Data Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email ndkrom@noble.org for more information.
Please be sure to complete these surveys before and after the workshop.
| 9:00 | Introduction to cloud computing for genomics |
| 9:15 | Logging onto Cloud |
| Shell genomics | |
| 9:30 | Introduction to the command line |
| 10:00 | Navigating Files and Directories |
| 10:30 | Break |
| 11:00 | Working with Files and Directories |
| 12:00 | Lunch |
| 13:00 | Redirection |
| 13:45 | Writing Scripts |
| 14:30 | Coffee |
| 15:00 | Project Organization |
| 15:45 | Wrap-up |
| 16:00 | END |
| Morning | Project organization and management |
| 09:00 | Welcome and workshop introductions |
| 09:30 | Data Tidiness |
| 10:00 | Planning for NGS Projects |
| 10:30 | Examining Data on the NCBI SRA Database |
| 10:45 | Coffee |
| Late morning | Data wrangling and processing |
| 11:00 | Assessing Read Quality |
| 12:00 | Lunch break |
| 13:00 | Trimming and Filtering |
| 13:45 | Coffee |
| 14:30 | Variant Calling Workflow |
| 15:00 | Automating a Variant Calling Workflow |
| 16:00 | END |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a Data Carpentry workshop, you will need access to the software described below and an up-to-date web browser.
For this workshop we will be using CyVerse Atmosphere cloud, so you need to register for CyVerse to access their cloud during workshop.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.