Home

Welcome to EPP622, Fall 2022!

The purpose of this site is to provide a resource for students and instructors participating in the course. It's easier for me to update and build labs than Canvas.

Syllabus Version 1

Quick Log In

ssh [email protected]

Quick Schedule

Day	Date	Topic	Format
Thursday	August 25	Command Line I	Online Only. Consider attending PRC.
Tuesday	August 30	Command Line II	In person.
Thursday	September 1	Command Line III	Online Only. Football parking mess.
Tuesday	September 6	Command Line IV	In person.
Thursday	September 8	Command Line V	In person.
Tuesday	September 13		No class. Work on Test 1.
Thursday	September 15	Short Read Variation I	In person.
Tuesday	September 20	Short Read Variation II	In person.
Thursday	September 22	Short Read Variation III	In person.
Tuesday	September 27	Short Read Variation IV	In person.
Thursday	September 29		No class. Work on Test 2. Consider attending PRC.
Tuesday	October 4		No class. Work on Test 2.
Thursday	October 6		No class. UTK Holiday.
Tuesday	October 11	Long Reads I	In person.
Thursday	October 13	Long Reads II	In person.
Tuesday	October 18	Long Reads III	In person.
Thursday	October 20	Long Reads IV	In person.
Tuesday	October 25	ISAAC	In person.
Thursday	October 27		No class. Work on Test 3. Consider attending PRC.
Tuesday	November 1		No class. Work on Test 3.
Thursday	November 3	RNA I	In person.
Tuesday	November 8	RNA II	In person.
Thursday	November 10	RNA III	In person.
Tuesday	November 15	RNA IV	In person.
Thursday	November 17	FAIR I	Online Only. Consider attending PRC.
Tuesday	November 22	FAIR II	In person.
Thursday	November 24		No class. UTK Holiday.
Tuesday	November 29		No class. Work on Test 4.
Thursday	December 1		No class. Work on Test 4.

Course Materials

Class 1 - 6 - Linux CLI Intro

Class 7 - 12 - Short reads and variation

Class 13. Tuesday, October 11, Long Reads I (In person.)

• Slides: Long Reads
• Reading: Opportunities and challenges in long-read sequencing data analysis - Amarasinghe 2020
• Lab: Long Reads I - QC and Assembly
• Class & Lab Recording

Class 14. Thursday, October 13, Long Reads II (In person.)

• Slides: Reference Genomes
• Reading
  • Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm Cheng et al 2021
  • BUSCO: Assessing Genome Assembly and Annotation Completeness - Mathieu Seppey et al 2019
  • The Human Pangenome Project: a global resource to map genomic diversity - Wang et al. 2022
• Lab: Long Reads II - CONDA ; BUSCO, Dot Plots, SyRI
• Class Recording
• Lab Recording

Class 15. Tuesday, October 18, Long Reads III (In person.)

• Slides: Pangenomes
• Reading
  • Computational pan-genomics: status, promises and challenges - The Computational Pan-Genomics Consortium, 2018
  • Plant pan-genomes are the new reference - Bayer et al 2020
  • Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement - Khan et al 2020
• Lab: Long Reads III - Mapping, Structural Variants
• Class & Lab Recording

Class 16. Thursday, October 20, Long Reads IV (In person.)

• Slides
• Reading:
  • Inferring synteny between genome assemblies: a systematic evaluation - Liu et al 2018
  • A comparative genomics multitool for scientific discovery and conservation- Zoonomia Consortium 2020
• Software:
  • Orthofinder: OrthoFinder: phylogenetic orthology inference for comparative genomics - Emms and Kelly 2019
  • MCScanX: MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity - Wang et al 2012
  • GeneSpace: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes - Lovell et al 2022
  • SyRI: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies - Goel et al 2019
  • Plotsr: [plotsr: visualizing structural similarities and rearrangements between multiple genomes](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0] - Goel et al 2022
• Test 3 - Due midnight Nov 3
• Lab: Long Reads IV - Comparing other genomes with Syri and RIdeogram
• [Class & Lab Recording]
• Screen
  • Screen instructions - the FULL docs
  • Screen cheatsheet - one of many out there, more convenient for casual use

Class 17. Tuesday, October 25, ISAAC (In person.)

• Slides: ISAAC (Meg)
• Lab: ISAAC Intro

Class 18. Thursday, October 27, (No class. Work on Test 3. Consider attending PRC.)

• ASSIGNMENT 3

Class 19. Tuesday, November 1 (No class. Work on Test 3.)

Class 20. Thursday, November 3, RNA I (In person.)

• Slides: RNASeq
• Lab: RNASeq I - QC, Mapping w/ STAR
• Screen

Class 21. Tuesday, November 8, RNA II (In person.)

• Slides: Project Design, GFF (Meg)
• Lab: RNASeq II - Salmon, tximport

Class 22. Thursday, November 10, RNA III (In person.)

• Slides: Normalization, Data Exploration (Meg)
• Lab: RNASeq III - DESeq2, EdgeR

Class 23. Tuesday, November 15, RNA IV (In person.)

• Slides: ABD3: Biological databases and types of data (Beant)
• Lab: RNASeq IV - Functional enrichment

Class 24. Thursday, November 17, FAIR I (Online Only. Consider attending PRC.)

• Slides: ABD4: Finding and obtaining data (Meg or recording)
• Lab: FAIR I

Class 25. Tuesday, November 22, FAIR II (In person.)

• Slides: ABD5: Submitting data, DMPs (Meg or recording)
• Lab: FAIR II

Thursday, November 24, No class. UTK Holiday.

Class 26. Tuesday, November 29, (No class. Work on Test 4.)

ASSIGNMENT 4

Class 27. Thursday, December 1 (No class. Work on Test 4.)