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      Genome-Wide Association Studies

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
Dr. Anthony Musolf Talk
What is Bioinformatics/Genomics?
Support
Slack
Zoom
Cheat Sheets
Software and Links
Scripts
Prerequisites
Logging In
CLI
R
Cluster Computing
Data Reduction
Files and Filetypes
Project setup
Preprocessing raw data
Alignment with BWA
Variant calling using GATK
Comparison of freebayes, GATK, and deepvariant output
Data Analysis
Plink Step by Step TDT
Plink Step by Step TDT (solutions)
wAnnovar Annotation
Plink Step by Step (Non FBAT excercise)
Setup in R
GWAS Visualization
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Logging In & Transferring Files

You should already have an account on our systems

For Macs/Linux - Logging In

  1. Open a Terminal (usually under Applications/Utilities on a Mac), or install iterm2
  2. Cut and paste this into the terminal:

     ssh username@tadpole.genomecenter.ucdavis.edu
    

    where ‘username’ is replaced with your username. Press Enter.

  3. Type in your password. No characters will display when you are typing. Press Enter.

For Macs/Linux - Transferring files

  1. Use scp (secure copy, a remote file copying program):

     scp username@tadpole.genomecenter.ucdavis.edu:full/path/to/file .
    
  2. Replace ‘username’ with your username and replace ‘full/path/to/file’ with the full path to the file you want to transfer. Note that there is a “.” at the end of the command, which is where to put the file, i.e. your current directory. You will have to type in your password.

For Windows - Logging In

Windows needs a terminal to connect with, you have a few options:

  1. Shell for Windows 10
  2. Enable SSH OR
  3. MobaXterm
  4. PuTTY

In putty, mobaxterm:

  1. Open up terminal.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Make sure the Connection Type is SSH.
  4. Press “Open”. It will ask you for your username and password.

    In Shell with SSH enabled:

     ssh username@tadpole.genomecenter.ucdavis.edu
    

    where ‘username’ is replaced with your username. Press Enter.

For Windows - Transferring files

  1. Open up WinSCP. If you haven’t installed it, get WinSCP here.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Type in your username and password.
  4. Make sure the File Protocol is SFTP.
  5. Press “Login”.