De novo RNAseq Assembly

Who: Titus Brown, lead instructor.

When: March 30, 2016

Times: 9:15am-12:15pm PST

Where: DSI Space, Shields Library UC Davis campus

Contact Jessica Mizzi with any questions.


This workshop will cover the assembly of de novo RNAseq data, focusing on non-model organisms. We will use a stock data set and do analysis on the Amazon cloud.

Installation Instructions

For this workshop, you need an AWS account and a terminal.

AWS account

Please make sure to register for an Amazon Web Services account. Step by step instructions for this process are provided here. Attendees will need to provide a credit card and cover their own computing costs, which should be less than $5 for the entire workshop. You should see an “Amazon Web Services” menu page, and see an “EC2” button on the top left corner after signing in.

IMPORTANT: You need to create this account at least 2 days before the workshop if you are creating a new account in order to be able to participate in the workshop because of a 2 day wait step in Amazon’s verification process.

Terminal Program


  1. Download the Git for Windows installer here.
  2. Follow install instructions.
    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Select “Use Git from the Windows Command Prompt” and click on “next”. If you forget to do this, re-run the installer and select the correct option.
    • Click “next”, keep “Checkout Windows-style, commit Unix-style line endings” selected.
    • Select “Use Windows’ default console window” and click on “next”
    • Click on “next”
    • Click on “finish”

Mac OS X:

The default shell in Mac OS X is bash, so you can access the Terminal from /Applications/Utilities (go to your Applications folder, then go to the Utilities window. You should see “Terminal” there)

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