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BZ360 Fall 2022 Schedule
| Topics | Reading/Videos | Assignments | |
|---|---|---|---|
| Week 1 (8/23, 8/25) | |||
| Tuesday | Introduction to Bioinformatics and Genomics slides | ||
| Thursday | Genetic Variation and Sequence alignments slides | PCR Genetic variation SNPs | Assignment 1 |
| Week 2 (8/30, 9/1) | |||
| Tuesday | Next Gen Sequencing (NGS) Technologies slides | Illumina PacBio Nanopore 10xGenomics Sequencing technologies | |
| Thursday | Command Line Computing Part 1 slides | Assignment 2 | |
| Week 3 (9/6, 9/8) | |||
| Tuesday | NGS Quality Control slides | FastQC | Assignment 3 |
| Thursday | Adapter Trimming and Quality Filtering slides | Assignment 4 | |
| Week 4 (9/13, 9/15) | |||
| Tuesday | Read Alignment slides | Mapping NGS reads | Assignment 5 |
| Thursday | Genomes and Genome Assembly slides | Genome sequencing The human genome Genome diversity | |
| Week 5 (9/20, 9/22) | |||
| Tuesday | Genome Assembly Cont. slides Review | Assignment 6 | |
| Thursday | Exam 1 | ||
| Week 6 (9/27, 9/29) | |||
| Tuesday | Command Line Computing Part 2 slides | Assignment 7 | |
| Thursday | Bash Scripts slides | Code Stars Programming Just for fun | Assignment 8 |
| Week 7 (10/4, 10/6) | |||
| Tuesday | Computers and Programs slides | Inside a computer Computer memory Hard drives | Assignment 9 mario pacman nerf |
| Thursday | Reproducibility and Version Control slides | Assignment 10 | |
| Week 8 (10/11, 10/13) | |||
| Tuesday | Bioinformatic Workflows slides | Algorithms | Assignment 11 |
| Thursday | Snakemake part 1 slides | Workflow languages | Assignment 12 |
| Week 9 (10/18, 10/20) | |||
| Tuesday | Snakemake part 2 slides | Assignment 13 | |
| Thursday | Snakemake part 2 cont. | Assignment 13 cont or Optional Assignment |
|
| Week 10 (10/25, 10/27) | |||
| Tuesday | TBD Review | ||
| Thursday | Exam 2 | ||
| Week 11 (11/1, 11/3) | |||
| Tuesday | Introduction to RNA-seq slides | NGS applications | |
| Thursday | Reference Data and Databases slides | Assignment 14 | |
| Week 12 (11/8, 11/10) | |||
| Tuesday | RNA-seq: quality control and filtering slides | RNA-seq | Assignment 15 |
| Thursday | RNA-seq: read alignment slides | STAR | Assignment 16 |
| Week 13 (11/15, 11/17) | |||
| Tuesday | RNA-seq: quantification slides | RSEM opportunities | Assignment 17 |
| Thursday | R slides | Assignment 18 | |
| Week 14 (11/22, 11/24) | |||
| Thanksgiving break | |||
| Thanksgiving break | |||
| Week 15 (11/29, 12/1) | |||
| Tuesday | RNA-seq: differential gene expression analysis slides | DESeq DESeq2 Tutorial | Assignment 19 |
| Thursday | RNA-seq: data visualization slides | IGV | Assignment 20 |
| Week 16 (12/6, 12/8) | |||
| Tuesday | RNA-seq: recap and review slides | Assignment 21 | |
| Thursday | Exam 3 |
schedule.txt · Last modified: 2022/12/06 19:30 by dokuroot
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