Short Read Trimming and Quality Evaluation

Who: Titus Brown, lead instructor.

When: March 28, 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 trimming and quality evaluation of short read RNAseq data. We will use a stock data set and do analysis on the Amazon cloud.

This workshop will be broadcast via YouTube for those who wish to participate remotely.

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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