Public genomic repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), and the European Nucleotide Archive (ENA) are invaluable resources but can be challenging to use due to their diverse structures, metadata formats, and download protocols. This workshop introduces key tools and workflows for accessing raw sequencing data from major public databases to work with on Quest. Participants will learn how to map between GEO and SRA accessions and retrieve metadata and sequence files using command-line tools. We will also discuss best practices for data management, metadata parsing, and troubleshooting common issues in retrieval workflows.

Prerequisite: This workshop requires a laptop with a terminal application installed and expects familiarity with working from the command line or attendance at the Command Line Introduction workshop.

About the series: This workshop series is designed to cover foundational topics in computational genomics for the research community that uses the Genomics Compute Cluster (GCC) at Northwestern. Most workshops can be attended ad hoc, but some of the content builds on itself from week to week, and most require attendance at the first workshop of the series, Command Line Introduction, so please read the description of each. These workshops will be held in person on the Chicago campus. To participate fully, you will need to bring a laptop with you to each workshop.

GCC Foundations: Getting Genomic Data Onto Quest (Chicago)