UC Davis Bioinformatics Core
Resource:: UC Davis RNA-Seq and ChIP-Seq Analysis with Galaxy Workshop Types:: Tutorial, Datasets, AMI Domains:: Quality Control, RNA-Seq, ChIP-Seq Owners:: UC Davis Bioinformatics Core Formats:: Entire workshop package Date:: 2014/12

This is a complete package of slides, examples, datasets, and an accompanying Amazon Machine Image.


All documentation is online:


  • General Comments - lecture
  • Sequencing Technologies - lecture
  • Introduction to Amazon Web Services EC2
  • Intro to Galaxy, and Illumina Read Grooming - lecture and exercises
  • Using FTP with Galaxy - exercise


  • Introduction to ChIP-Seq - lecture
  • Read Alignment - lecture and exercise
  • ChIP-Seq Data Analysis - lecture
  • ChIP-Seq Analysis - exercise
  • Visualizing ChIP-Seq data on the UCSC Genome Browser - exercise


  • RNA-Seq Concepts, Terminology, and Work Flows - lecture
  • Aligning SE RNA-Seq Reads to a Reference Genome - exercises
  • Aligning PE RNA-Seq Reads to a Genome - exercises
  • Gene Construction and the Tuxedo Suite - lecture
  • Alignment to a Reference Transcriptome - exercises
  • Differential Expression Analysis with edgeR from Genome Alignments - exercises
  • RNA-Seq Statistics - lecture
  • Some Helpful Links


  • I’ve Done My Analysis, Now What? - discussion
  • Odds & Ends (unanswered questions from earlier) - lecture
  • Multifactorial Analyses with edgeR - demo

See the workshop documentation home page for links.

Needed Tools

The easiest way to use this material is launch the workshop's accompanying Amazon Machine Image (AMI): ami-ab010aee. It has all needed tools already installed on it. See the UC Davis Bioinformatics Core Software page for details.


The workshop AMI (ami-ab010aee) also includes the example datasets used in the exercises.