Bioinformatics Genomics Data Workshop

Date: April 12, 2017 9am-4pm

Location: Information Technology Center Room 105A/B, UH Manoa

Presenters: John Fonner (TACC), Sean Cleveland(UH), Joe Stubbs (TACC), Rion Dooley (TACC), Ron Merrill (UH), David Schanzenbach (UH), and Jennifer Geis(UH)

This FREE workshop is sponsored by the University of Hawai’i Information Technology Service Cyberinfrastructure group, the Texas Advance Computing Center and Hawai’i EPSCoR.

This workshop is designed for researchers working with genomics data and teaches basic concepts, skills and tools. No prior computational experience is required

The focus will be on data management and analysis for genomics research. We will cover metadata organization, data organization, connecting to and using advanced computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline. By the end of the workshop learners should be able to manage and analyze data more effectively and be able to apply the tools and approaches directly to their ongoing research.

Participants should bring their laptops and plan to participate actively. Laptops will require a terminal application for accessing compute resources - Linux and Mac machine have this already, for Windows machines we recommend the free home version of MobaXterm. We will also be using jupyter notebooks- at the moment Microsoft is offering free Azure hosted jupyter notebooks so please create a Microsoft account prior to the workshop if you do not have one already.

The Workshop is at capacity and is no longer accepting participants. Please be on the look out for future opportunities.

Workshop structure

One dataset will be used throughout the workshop. We will start by introducing the dataset and the steps we’ll go through for analysis.

Dataset

In this workshop we’re using data from Blount et al 2012 paper from Dr. Richard Lenski’s Long Term Evolution Experiment.

• Overview of the dataset

Workshop Timeline

Start Time	Topic
9:00am	Introduction
9:10am	The Dataset
9:20am	Metadata and Data Organization
9:30am	Introduction to the command line
10:00am	Break - coffee and light refreshments provided
10:15am	Command line Continued
11:00am	Data Wrangling
Noon	Lunch - on your own
1:00pm	Introduction to R
2:15pm	Break - coffee and light refreshments provided
2:30pm	Agave/ToGo
4:00pm	End

Etherpad

https://public.etherpad-mozilla.org/p/UH-bioworkshop

Workshop Materials

• Overview
• Introducing the dataset and questions
• Genomic data in the NCBI SRA database

Metadata and Data Organization

• Metadata Lesson
• Think about and understand the types of data and metadata a sequencing experiment will generate
• Gain a general understanding of data organization

Introduction to the command line

• Overview
• Connecting
• The file system
• Searching files

Data wrangling and processing

• Project Setup
• Quality control of NGS data
• Automating a workflow
• Optional Advanced Exercise Variant calling workflow

R for data analysis and visualization

• Before Getting Started
• Introduction to R
• Starting With Data
• Data Frames
• Dplyr
• Data Visualization With R
• Scripting With R

Agave/ToGo

• Introduction to Agave ToGO
• Registering Systems
• Creating Apps