Data Carpentry Genomics Workshop - University of Nevada, Reno

Jan 15-16, 2019

9:00 am - 5:00 pm

Instructors: Elias Ozolor, Sateesh Peri

Helpers: Richard Tillett, Gurlaz Kaur, Jeremiah Reyes, Ning Chang, Kyle Wang

This is the official website for the upcoming Data Carpentry Genomics Workshop at University of Nevada, Reno (January 15-16th, 2019). This workshop is free for attendees and is supported by funding from UNR Libraries and NV-INBRE.

Registrations for this workshop have closed.

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 target audience is students (both undergraduate and graduate) who have little to no prior computational experience. The instructors will prioritize creating a friendly environment that will empower researchers and enable data-driven discovery. Even those with some experience will benefit, as the goal is to teach not only how to do analyses, but how to manage the process to make it as automated and reproducible as possible.

Where: Room 107, Mathewson-IGT Knowledge Center, 1664 North Virginia St, Reno, NV 89557. Get directions with OpenStreetMap or Google Maps.

When: Jan 15-16, 2019. Add to your Google Calendar.

Food: Lunch, coffee, and snacks for both days will be provided free of cost. (Yay!)

Registrations for the workshop have closed. The registrations and wait-list for this workshop are currently full. Wait-listed candidates will be informed if there are any drop-outs by January 6th 2019.

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 perisateesh@nevada.unr.edu or eazadbakht@unr.edu 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

09:00-09:45am Introduction and Genomics Workshop Overview
9:45-10:30am Introduction to CyVerse Atmosphere Cloud
10:30-10:45am Coffee/Tea break
10:45-12:00pm BASH- Command Line for Genomics
12:00-1:30pm Lunch Break (lunch will be provided!)
1:30-2:45pm BASH - continued and Bioconda
2:45-3:00pm Coffee/Tea Break
3:00-4:00pm RNAseq overview and Trimming sequencing data
4:00-5:00pm Version control with Github

Day 2

09:00-10:30am Transcriptome Assembly
10:30-10:45am Coffee/Tea Break
10:45-12:00pm Read Quantification
12:00-1:30pm Lunch Break (lunch will be provided!)
1:30-2:30pm Differential Expression and GO analysis
2:30-2:45pm Coffee/Tea Break
2:45-5:00pm Project Organization and Markdown

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

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 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.

The Bash Shell

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

Windows

  1. Download and install PuTTY for Windows .

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). 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.