-
Notifications
You must be signed in to change notification settings - Fork 1
Home
Meg Staton edited this page Aug 21, 2024
·
105 revisions
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.
- ISAAC-UTK0318
- qos=class; partition=condo-epp622
| 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. |
Class 1 - 6 - Linux CLI Intro
Class 7 - 12 - Short reads and variation
Class 13 - 16 - Long Reads
- No Slides
- Lab: ISAAC Intro
- Recordings - Part 1 and Part2
- Lots more instructional videos from OIT
- ASSIGNMENT 3
- AgBioData Video- FAIR databases
- Slides: RNASeq Intro
- Lab:
- 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
- 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
- Slides: Normalization, Data Exploration
- Lab: RNASeq II - Salmon
- Class & Lab Recording
- Slides: DMPs and TRUST
- Lab: RNASeq IV - DESeq2 with star, DESeq2 with salmon
- Class & Lab Recording 30-40s pause starting at 04:14 due to network interruption!
- Slides: Ontologies and Submitting Data
- Lab: Finish tximport and DESeq2 of salmon quants from last time.
- Reading:
- Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery Jensen and Bork 2010
- https://www.nature.com/articles/s41597-020-0524-5 Schriml 2020
- Recording