This is a complete package of slides, examples, datasets, and an accompanying Amazon Machine Image.
- 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.
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.
- UC Davis RNA-Seq and ChIP-Seq Analysis with Galaxy Workshop
- Using Galaxy for Analysis of High Throughput Sequence Data course offered at the UC Davis Bioinformatics core, June 16-20, 2014
- UC Davis Bioinformatics Core Software page
- UC Davis Bioinformatics Training Program FAQ
- Amazon Web Services
- 2013 UC Davis Galaxy Course Documentation