Accessing genomic reference and experimental sequencing data
| Audience | Computational skills required | Duration |
|---|---|---|
| Biologists | Beginner bash | 3 hour workshop (~3 hours of trainer-led time) |
Description
This repository has teaching materials for a 3 hour, hands-on Accessing genomic reference and experimental sequencing data workshop led at a relaxed pace.
For many types of sequencing analyses, we need access to public data stored in various databases and repositories. This workshop will discuss types of genomic reference data available through public databases such as Ensembl, NCBI, and UCSC, and step through how to find and download this data. The workshop will also explore how to find and download publicly available experimental data, such as data (FASTQ files and count matrices) from published papers, using GEO and the SRA repositories. While most of the workshop will access data using a web browser, downloading data from the SRA will require beginner knowledge of the command-line interface.
Learning Objectives
- Understanding what is a genome build
- Identifying differences in reference data available from Ensembl, NCBI, and UCSC
- Finding and downloading experiment-appropriate genome reference data
- Finding and downloading publically available experimental sequence data
These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.
Lessons
- Click here for links to lessons and the suggested schedule using the HMS-RC O2 cluster
- Click here for links to lessons and the suggested schedule using the FAS-RC Odyssey cluster
Dataset
We will be demonstrating how to access the data in the lessons.
Installation Requirements
Mac users: No installation requirements.
Windows users: GitBash
These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.