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Welcome to EPP622, Fall 2024!
Peer Review - Fill out and submit to get credit for peer reviewing. For full credit you will need to provide at least one constructive comment about each presentation. "Nice job" and "good job" do not count.
Quick Log In
ssh [email protected]
Isaac info:
- Project: ISAAC-UTK0318
- qos=class
- partition=condo-epp622
ssh [email protected]
cd /lustre/isaac/proj/UTK0318
Quick Schedule
| Topic | Class Format | |||
|---|---|---|---|---|
| 1 | Tuesday | August 20 | Command Line I | In person and recorded. |
| 2 | Thursday | August 22 | Command Line II | In person and recorded. |
| 3 | Tuesday | August 27 | Command Line III | In person and recorded. |
| 4 | Thursday | August 29 | Command Line IV | In person and recorded. |
| 5 | Tuesday | September 3 | Command Line V | In person and recorded. |
| 6 | Thursday | September 5 | No new material. | Optional work on Test 1 in class. |
| 7 | Tuesday | September 10 | Short Read Variation I | In person and recorded. TEST 1 Due at midnight. |
| 8 | Thursday | September 12 | Short Read Variation II | In person and recorded. |
| 9 | Tuesday | September 17 | Short Read Variation III | In person and recorded. |
| 10 | Thursday | September 19 | Short Read Variation IV | In person and recorded. |
| 11 | Tuesday | September 24 | Short Read Variation V | In person and recorded. |
| 12 | Thursday | September 26 | No new material. | Optional work on Test 2 in class. |
| Tuesday | October 1 | No new material. | Optional work on Test 2 in class. | |
| 13 | Thursday | October 3 | ISAAC | In person and recorded. TEST 2 Due at midnight. |
| 14 | Tuesday | October 8 | No Class | Fall Break |
| 15 | Thursday | October 10 | ISAAC | In person and recorded. |
| 16 | Tuesday | October 15 | Long Reads I | In person and recorded. |
| 17 | Thursday | October 17 | Long Reads II | In person and recorded. |
| 18 | Tuesday | October 22 | Long Reads III | In person and recorded. Project proposal due at midnight. |
| 19 | Thursday | October 24 | Long Reads IV | In person and recorded. |
| 20 | Tuesday | October 29 | No new material. | Optional work on Test 3 in class. |
| 21 | Thursday | October 31 | No new material. | Optional work on Test 3 in class. |
| 22 | Tuesday | November 5 | No Class | Election Day |
| 23 | Thursday | November 7 | No new material. | Optional work on project in class. TEST 3 Due at midnight. |
| 24 | Tuesday | November 12 | No new material. | Optional work on project in class. |
| 25 | Thursday | November 14 | No new material. | Optional work on project in class. |
| Tuesday | November 19 | No new material. | Optional work on project in class. | |
| 26 | Thursday | November 21 | No new material. | Optional work on project in class. |
| 27 | Tuesday | November 26 | FINAL PROJECT PRESENTATIONS | In person. Attendance required. |
| 28 | Thursday | November 28 | No Class | Thanksgiving |
| 29 | Tuesday | December 3 | FINAL PROJECT PRESENTATIONS | In person. Attendance required. |
OIT Bioinformatics Symposium and Isaac Trainings (Not required, just here for your information or if you want to get a jump start)
Full Schedule
Classes 1-6 - Intro to command line
Classes 7-13 - Variant Calling
Class 14. Thursday October 3 - Introduction to ISAAC-NG
- In person and recorded. TEST 2 Due at midnight.
- Lab: ISAAC‐NG Intro
- Slides
- Class Recording
Class 15. Thursday October 10 - ISAAC‐NG Continued
- In person and recorded.
- Lab: ISAAC‐NG Continued
- Class Recording
Class 16. Tuesday October 15 - Long Reads I
- In person and recorded.
- Talk about Final Project. Send a proposal via canvas by Tuesday October 22. Proposal should be less than one page and cover your general idea
- Slides: Long Reads and Conda
- Reading:
- Method of the year: long-read sequencing Marx, 2024
- Genomics in the long-read sequencing era van Dijk et al, 2023
- Conda Cheat Sheet
- Lab: Long Reads I - Install Conda and Long Read QC
- Class & Lab Recording
Class 17. Thursday October 17 - Long Reads II
- In person and recorded.
- Slides: Structural Variants
- Reading/Viewing
- Lab: Long Reads II - Long Read Mapping and Calling SVs with CuteSV
- Class and Lab Recording
Class 18. Tuesday October 22 - Long Reads III
- In person and recorded.
- Final project - link at top of page, presentation slots assigned, proposal submission open
- Slides: Genome Assembly
- Reading
- Lab: Long Reads II - Go back to previous lab to revisit
- qualimap stats
- visidata
- IGV
- Lab: Long Reads III - Genome Assembly
- Class & Lab Recording
Class 19. Thursday October 24 - DMPs and Long Reads IV
- In person and recorded.
- Slides: Data Management Plans
- Lab: Long Reads III - Finish Up
- Class and lab recording