Announcements
- December 2: The final exam is available here. It is due before midnight on 12/6. It is composed of 5 short-answer questions. All questions reference the paper: "From molecules to genomic variations: Accelerating genome an alysisvia intelligent algorithms and architectures." Collaboration and communication with other BCB716 students past or present is strictly prohibited. If any question seems to be unclear or incomplete, state a reasonable assumption and continue.
- November 22: Unfortunately, I will need to cancel today's class. The founder of my department passed on Thursday evening, and I will be attending a memorial servvice for him during the schedued class-time. I have created accounts for everyone, but I have not had the time to post problem sets. Keep an eye out and I will figure out something for next Tuesday.
- November 15: Another day and the problem sets are still broken. I plan to make dome dramtic changes on Thursday. Stay tuned.
- November 3: Professor Jeremy Wang will be giving today's lecture in Marsico 2004.
- October 27: The first day of class. See you there.
Course Description
This module is designed to introduce students to concepts and methods in the comparative analysis of nucleic acid sequences using state of the art sequencing platforms. Course topics will include sequence alignment, genome assembly, and computational details of contemporary protocols for DNA and RNA sequencing.
Course Information and Grading
This semester I will not be using a book. I will be teaching from my own slides and notes.
| Credit Hours: | 1 |
| Location: | Marsico 2004 |
| Time: | TTh 11:00am-12:15pm |
| URL: | http://www.csbio.unc.edu/mcmillan/?run=Courses.BCB716F22 |
Course Instructor
| Instructor: | Leonard McMillan |  |
| Office: | SN316 | |
| email: | mcmillan@cs.unc.edu | |
| Office Hours: | Mondays 3pm-4pm |
Schedule
| Date | Topic | Homework |
| October 27 (Th) | Lecture 1.Introduction to Genomes (slides) | |
| November 1 (T) | Lecture 2. Sequencing Technologies (slides) | |
| November 3 (Th) | Lecture 3. DNA Alignment Methods and Analysis (slides) | |
| November 8 (T) | Lecture 4. DNA Analysis using IGV (slides) | PS #1 |
| November 10 (Th) | Lecture 5. DNA Variant Calling (slides) | |
| November 15 (T) | Lecture 6: RNA Sequencing and Methods (slides) | PS #2 (PS #1 due) |
| November 17 (Th) | Lecture 7. RNAseq Analysis (slides) | |
| November 22 (T) | Lecture 8. TBD | PS #3 (PS #2 due) |
| November 24 (Th) | Thanksgiving Break | |
| November 29 (T) | Lecture 9. New Approaches to *seq Analysis (slides) | (PS #3 due) |
| December 1 | Final Exam must be turned in before 12/6 at 5pm |
|
Resources
Alternate Way to Access IGV:
If the Longleaf Desktop Interactive Session does not load properly for you, but you are able to access the OnDemand Portal, try the following:
1. Click on the Interactive Apps tab and select the Firefox GUI.
2. Launch the session and go to https://igv.org/app/ .
3. Under the Genome tab on the IGV web GUI, select the appropriate reference genome (i.e. Mouse(GRCm38/mm10)).
4. Then load your sample file of interest using the Tracks tab -> Local File -> on the left hand side of the File Upload window, scroll down to +Other Locations -> Computer -> proj -> mcmillanlab -> BCB716F21 -> path to file.
5. Make sure to load both the .bam and .bai files!