Past RNA-Seq Workshops – The Broad Institute

De novo & Genome-guided Transcript Reconstruction from RNA-Seq

Participants in this workshop will learn the basics of how to reconstruct and analyze transcriptomes starting from RNA-Seq data using genome-guided and genome-free methods. Genome-guided reconstruction will be performed using the Tuxedo software suite, and genome-free reconstruction will use Trinity. The course consists of a lecture followed by direct exploration of sample RNA-Seq data using the tools in the context of each analysis framework.

December 2

Genome View (Part I)

This workshop will teach you how to get started with GenomeView, an interactive genome browser and annotation editor. It allows you to visually explore various data types that come out of (comparative) genomic studies. This includes references genomes with annotation, sequence reads, read coverage, whole genome alignments with translated annotations and read based variation. You will learn how to prepare your data for visualization, how to get started with the various visualization tracks and you will get some tips and tricks on how to leverage read data, annotations and whole genome alignments to verify your data generation and downstream analyses. Finally we’ll explore how you can use this to generate hypotheses by leveraging the various visualizations.The workshop will start with an introductory presentation and a step-by-step walkthrough of some of the most salient features with interactive examples. After the walkthrough, participants can either complete tutor guided exercises with the example data or can explore their own data with the newly learned skills. The examples during the workshop will focus on non-vertebrate genomes, i.e. plants, fungi, and bacteria, but are equally applicable to any other genomes. The examples will include data from various types of sequencing assays: ChIP-seq, RNA-seq and WGS. We will also highlight visualizing different comparative genomics analyses with two examples. The first one will look at read based genome diversity through variant calls. The second one will look at whole-genome based comparative studies. Example data sets will be provided.Participants should bring their own computer and participants are very much encouraged to bring their own data in any of the supported file formats.

October 22

Intro to RNA-Seq

RNA-Seq is revolutionizing our ability to analyze the transcriptome. This seminar will present participants with an overview of RNA-Seq principles, experimental considerations, steps of the RNA-Seq analysis process, and current state of the art. It will provide the basis for future in-depth RNA-Seq courses and workshops.

May 7 Workshop Materials

RNA-Seq Basics

This workshop will cover the basic conceptual ideas behind library construction, sequencing, and initial analysis of RNA-Seq data. The workshop is aimed at biologists who want to learn the basics of RNA-Seq analysis, computationalists who want to understand more about the basics of RNA-Seq data generation, or anyone who is interested in RNA-Seq but is not familiar with basic high throughput sequencing technologies. We will start with very basic concepts from three perspectives: generating high throughput (e.g., Illumina) sequencing data; making RNA-Seq libraries; and understanding mRNA structure, annotation, and quantitation. We will proceed through the steps of basic sequencing into the common first pass methods for analysis. Prospective attendees who are already familiar with the majority of these concepts and are looking for a more in depth or hands-on workshop on specific RNA-Seq techniques are advised to look for our more advanced workshop in May.

March 6 Workshop Materials

Differential Expression analysis of RNA-Seq with the Tuxedo Tools

RNA-Seq is now a routine assay for measuring gene expression, but the analysis of the data can be daunting. This course will cover basic principles of RNA-Seq analysis and include hands-training for the “Tuxedo Tools”. Users will learn to run TopHat, Cuffdiff, and CummeRbund to detect differentially expressed genes and transcripts.Objective
Participants in this workshop will learn fundamental concepts of RNA-Seq analysis and be able to perform a basic differential analysis at gene- and isoform-resolution using the Tuxedo Tools.Skill Level
Those new to RNA-Seq. Familiarity with UNIX and/or R is a strong plus.

Users are strongly encouraged to familiarize themselves with R prior to coming to the workshop. You will get much more out of this workshop if you are comfortable with starting and stopping an R session and performing very simple tasks such as opening and viewing files in R.

Users are also encouraged to have a look at ggplot2, which is a beautiful plotting package written in R. CummeRbund, which we will use to explore our RNA-Seq data, is built on top of ggplot2.

There is an excellent, easy to read book on ggplot2, and you can find sample chapters here: Chapter 2 is available for free, and you are strongly encouraged to try running the bits of R code in chapter 2 on your own to get a feel for what exploring data with R and ggplot2 is like. The entire book is available through
and is an extremely worthwhile read.

January 11