The Huck Institutes of the Life Sciences

Bioinformatics 101: Simple and Efficient Genomic Data Analysis

This hands-on workshop will introduce the basics of data science and bioinformatics analysis. It includes three sessions: shell scripting, sequence alignment and high performance computing. Demo code will be provided, and the instructors will walk through each exercise step-by-step. Real world datasets will be used and participants will be able to explore bioinformatics within high performance computing resources
This workshop will begin with an introduc
tion to the Integrative Genomics Viewer (IGV) browser including:
Pre
-
processing your data for visualization.
Loading references and gene annotations.
Sharing your session with your collaborators.
After the introductory talk we will have three data centric
modules:
Transcriptome visualization and exploration.
Genome missassemblies
SNPs discovery and genome rearrangement

Event details

When: Sep 23, 2017

From: 2:30-5:30 PM

Where: Berg Auditoruim

Contact: Divyanshi Srivastava, dvs5680@psu.edu

Registration for the workshop:

Workshop registration option is provided in the retreat registration form.

Topics Covered:

  • Text file manipulation & shell scripting
  • Short read alignment & inference
  • Interfacing with High Performance Computing (HPC) clusters

 

Instructions:

Each session will be 1 hour, with 10-15 minutes of talks, and 45 minutes of guided hands on exercises. For all practical exercises, we will be working with the yeast genome, sg11. The data for the workshop is located here: https://github.com/PSUGenomix/BG_retreat_workshop_2017

To interface with HPC clusters, we require all participants to sign up for an ACI account. (ACI is Penn State’s HPC infrastructure).  Accounts need to be requested at least 3 days before the workshop, at the following link: https://accounts.aci.ics.psu.edu/users/

The sponsor account will be: css13@psu.edu

Please bring your laptop computer.