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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

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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 - 16 - Long Reads

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

• No Slides
• Lab: ISAAC Intro
• Recordings - Part 1 and Part2
• Lots more instructional videos from OIT

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.)

• AgBioData Video- FAIR databases
• Slides: RNASeq Intro
• Lab:
  • grep and sed - Not finished, try https://ryanstutorials.net/linuxtutorial/grep.php#examples and https://www.grymoire.com/Unix/Sed.html
  • RNASeq I - QC, Mapping w/ STAR
• Class & Lab Recording
• Readings
  • RNA Sequencing Data: Hitchhiker’s Guide to Expression Analysis - Van den Berge 2019
  • RNA sequencing: the teenage years - Stark et al 2019

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

• Slides: Project Design, GFF
• Lab: RNASeq II - gff/gtf, star mapping and counting, task array example
• Readings
  • Alignment and mapping methodology influence transcript abundance estimation- Srivastava et al 2020
  • Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences- Soneson et al 2016
• Class & Lab Recording

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

• Slides: Normalization, Data Exploration
• Lab: RNASeq II - Salmon, DESeq2 with star

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.)