Tutorials in Genomics & Bioinformatics: RNA-Seq Analysis
November 12 - 14, 2023

Instructors:

Delphine Fagegaltier, Merck Research
Benjamin King, University of Maine
Emily Hodges, Vanderbilt University School of Medicine
Steven Munger, The Jackson Laboratory

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COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination (within one year of the course’s start date) with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and Federal Guidelines applicable in Fall 2023.

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Tutorials in Genomics & Bioinformatics: RNA Seq is an intensive two-day introductory course to genomics and  bioinformatics. Participants are expected to arrive by 6 p.m. on the first day (Sunday November 12) with the course running two full days until 5 p.m. on the third day (Tuesday November 14).

TGB is modeled on Cold Spring Harbor Laboratory's  The Genome Access Course, a two day course normally offered in person at CSHL and other locations. TGB is broken into modules that are each designed to give a broad overview of a given topic, with ample time for examples chosen by the instructors. Each module features a brief lecture describing the theory, methods and tools followed by a set of worked examples that students complete. Ample opportunities will be designed for students to engage instructors virtually during the course with specific tasks or problems that pertain to their own research.

The core of the course is the analysis of sequence information framed in the context of completed genome sequences. Featured resources and examples primarily come from mammalian species, but concepts can be applied to any species. The course also features methods to assist the analysis and prioritization of gene lists from large scale microarray gene expression and proteomics experiments. 

TGB will provide hands-on experience by re-analyzing a published RNA-Sequencing data set.

Genome Browser Resources
  • Genome Annotation
  • Browsing Gene Function
  • Bulk Genome Analysis
Designing RNA-Seq Studies
  • Best practices in the design of bulk RNA-Seq studies. 
  • Caveats in analysis workflows 
Analysis of High-Throughput Sequence Data Using Galaxy 
  • Importing FASTQ files 
  • Importing reference genomes and annotation
  • Read quality control and diagnostics
  • Read trimming
Analysis of RNA-Seq Data 
  • Read mapping and quantification
  • Test for Differentially expressed genes using R/DESeq2
Gene Set Enrichment and Pathway Analysis
  • Gene set enrichment analysis using Gene Ontology and pathway annotations

Format

Each student will join the course virtually via zoom and slack, and thus should ensure they have full audio/video capability to engage in zoom meetings. Many of the exercises require common browsers such as Google Chrome, Microsoft Edge (formerly Internet Explorer), Mozilla Firefox, and Apple's Safari.  Both PCs and Macs are acceptable as long as they're updated with all security patches and bug fixes.

Target Audience

Tutorials in genomics & Bioinformatics is open to all on a first-come, first-served registration system. It is most beneficial for bench scientists transitioning into projects that require intensive analysis or integration of large data sets. The virtual course will introduce you to publicly available resources, and it will also help you develop a vocabulary that can be used to collaborate with computational scientists.

If you already have significant programming or data analysis experience, TGAC is not appropriate for you. For more detailed curriculum on methods used in computational biology, please see the Computational Genomics course. Students interested in the practical aspects of software development are encouraged to apply to the course on Programming for Biology. Students who would like in-depth training in the analysis of next-generation sequencing data (e.g., genome assembly and annotation, SNP calling, and the detection of structural variants) may be interested in the course on Advanced Sequencing Technologies. Finally, please see the course on Statistical Methods for Functional Genomics if you would like training in the statistical analysis of high-throughput genomics data.

Support

Major support is provided by the Helmsley Charitable Trust. Limited financial aid is available; please apply in writing to Olivia Mulligan describing your need for financial support.

       

Pricing:
Academic Package (two nights of housing/Single Room/Private Bath): $1,185
Academic Package (two nights of housing/Single Room/Communal Bath): $1,135
Academic Package (two nights of housing/Double Occupancy): $1,060
Corporate Package (two nights of housing/Single Room/Private Bath): $1,880
Academic No-Housing Package: $875
Corporate No-Housing Package : $1,570
Extra nights at $285 per night including food

All packages cover registration, food, coffee breaks, and a reception. Transportation to and from Cold Spring Harbor is not included. Full payment is due three weeks prior to the course.