Introduction

This course provides an introduction to the basics of using open source software tools to analyze large scale genomics data, specifically Next Generation Sequencing data.

In this course, you will learn general NGS workflow, data analysis pipeline, data formats, short read mapping and alignment software, general workflow for DNA-seq, RNA-seq and ChIP-seq. Data visualization tools will also be covered. Single Cell RNA-seq will be discussed.

Who: This course is designed for faculty, postdocs and graduate students who are working on genomics and other large analytical projects and want a quick introduction to Bioinformatics. It is recommended that you take the Intro to Linux workshop first.

Requirements: Participants must bring a laptop with a few specific software packages installed (see Pre-Workshop Instructions).

Prerequisites: Some programming experience is recommended.

Contact: Please mail jie.wu@uci.edu for more information.

Tentative Schedule

Syllabus

• NGS workflow
• NGS data analysis pipeline
• RNA-seq
• ChIP-seq
• Single Cell RNA-seq
• Data visualization

Pre-Workshop Instructions

Prerequisites for hands on session

a Mac, PC, or Linux laptop with wifi pre-registered with the UCI Mobile network a free HPC account

For windows users

Please install the “putty” terminal program (http://goo.gl/XbTF) and the Windows x2go client (http://code.x2go.org/releases/binary-win32/x2goclient/releases/4.0.0.3/x2goclient-4.0.0.3-setup.exe)

Registration