UC Davis - DIBSI Genomics

June 27-28, 2018

9:00 am - 4:30 pm

Instructors: Ryan Peek, Taylor Reiter, Shannon Joslin

Helpers: Azalee Bostroem, Rayna Harris, Mike Lee, Peri Sateesh

This is the website for the Genomics workshop to be run at DIBSI 2018. We will be updating the content below as the date of the workshop approaches. In the mean time:

Curriculum for this workshop may be viewed here: http://www.datacarpentry.org/genomics-workshop.

Registration for this workshop may be found here: https://registration.genomecenter.ucdavis.edu/events/DIBSI_2018_Genomics_Workshop

The etherpad for this workshop can be found here: http://pad.software-carpentry.org/2018-06-27-genomics

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: Gladys Valley Hall, Davis, California, 95616. Get directions with OpenStreetMap or Google Maps.

When: June 27-28, 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 dib-training@ for more information.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

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
Mid-MorningIntroduction to cloud computing for genomics: Part I
11:00 Why of cloud computing
11:05 Logging onto Cloud
11:15 Fine tuning your Cloud Setup
12:00 Lunch break
AfternoonIntroduction to the command line
1:00 Introducing the Shell
1:15 Navigating Files and Directories
13:45 Working with Files and Directories
14:30 Coffee
14:45 Redirection
15:30 Project Organization
16:15 Wrap-up
16:30 END

Day 2

Morning Data wrangling and processing
09:00 Assessing Read Quality
10:00 Trimming and Filtering
10:45 Coffee
11:00Variant Calling Workflow
12:00 Lunch break
13:00 Automating a Variant Calling Workflow
AfternoonIntroduction to cloud computing for genomics: Part II
14:30 Coffee
14:45 Data roundtripping
15:15 Which Cloud for my data?
16:15 Wrap-up
16:30 END

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Setup

To participate in a Data Carpentry workshop, you will need access to the software 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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

macOS

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). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

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.