Course Overview
Course Structure
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Short Lecture over a relevant topic
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Lab time, with an assignment teaching the related topic(Due next Tuesday?)
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Small toy project once a week for a grade(Replaces quizzes that got eaten alive last summer)
- If students are spending more than an hour on them reach out for help!
Overview
| Week | Date | |
|---|---|---|
| 1 | 5/28/24 | Class Cancelled due to weather |
| 5/30/24 | Introduction \ Lab: Intro to Unix | |
| 2 | 6/4/24 | Lab: Reproducible Research |
| 6/6/24 | Lab: Unix Data Analysis | |
| 3 | 6/11/24 | Lab: Snakemake pipeline |
| 6/13/24 | Lab: Snakemake pipeline | |
| 4 | 6/18/24 | Lab: Transcriptomics |
| 6/20/24 | Lab: nf-core | |
| 5 | 6/25/24 | Databases - UCSC genome browser, ENSEMBL |
| 6/27/24 | Lab: galaxy browser | |
| 6 | 7/2/24 | Lab: Cosmic database (online and R console) |
| 7/4/24 | no class - holiday | |
| 7 | 7/9/24 | Epigenomics |
| 7/11/24 | Lab: ChIP-seq | |
| 8 | 7/16/24 | Lab: ATAC-seq |
| 7/18/24 | Lab: methyl-seq | |
| 9 | 7/23/24 | Project work day |
| 7/25/24 | Project work day | |
| 10 | 7/30/24 | Project work day |
| 8/1/24 | Project Presentations | |
| 11 | 8/6/24 | Project Presentations |
Sections
- Weeks 1-4 - Intro to Unix and Computational Genomics, and Raw data pre-processing
- Weeks 4-7 - Databases and catalogs, Utilizing published data
- Weeks 9-10.5 - Galaxy Analysis, Final project presentation