Announcements

[Lecture Zoom Link] [Office Hours Zoom Link] [Nina Office Hours Zoom Link] [Dan's Office Hours Zoom Link]

• December 2: The final exam is now active at this link. I have extened the allowed time to 2 hours. You must complete the exam before 5pm on 12/3.
• December 2: I will lead today's lecture from my office rather than from MEJ 3106 to avoid any technical issues like those that occured last lecture.
• December 2: A link to today's in-class exercise and problem set #3. Once more I will go over the exercise in class first and then cover the lecture as time permits. The Final exam will be  linked to this website before 5pm. You can take it any time between then and 5pm on 12/3. Once downloaded you will have 90 mins to submit your answers. 
• November 30: A link to today's in-class exercise and problem set #2. I will go over the exercise in class. Make sure that you can start an interactive desktop on longleaf, run IGV, and have set your default genome to Mouse (mm10). 
• November 23: Due to my (LM) lack of preparation, I have decided to restructure how the problem sets and final will be administered this semester. The problem sets will be in the form of Google Forms. The first can be found here: Problem Set #1. Problem sets #2 and #3 will also be Google Forms and links will be posted here before class on 11/30 and 12/2 respectively. The problem sets will also take the form of in-class exercises on those same days. This means that class time will be alloted to complete them. Both the instructor and TAs will be provide assistance and answer questions. The Final Exam will also be a google form linked on the course website, and it will become available after class on 12/2 and must be completed within 90 mins of when it is downloaded. Your final exam must be submitted before 5pm on 12/3.



• November 22: Nina will not hold office hours on 11/26. Enjoy the day off!
• November 18: As of 11:04 I am having Zoom/Network problems in the MEJ classroom. I was able to get on zoom around 11:07, but no one appeared to hear me. I will try onece more
• November 16: The due date for the combined problem set #1/#2 has been changed to 11/23 
• November 11: Dan will hold office hours Tuesdays and Thursdays 1pm-2pm. See zoom link above.
• November 11: Nina will hold office hours Mondays 2pm-3pm and Fridays 1pm-2pm. See zoom link above. 
• November 10: I need to move my scheduled office hours this week from Wednesday to Thursday from 2pm-4pm. I would like to use this time primarily to help students get set up on Longleaf. The zoom link has been added above.

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.

Course Instructor

Instructor:	Leonard McMillan
Office:	SN316
email:	mcmillan@cs.unc.edu
Office Hours:	Wednesdays 2pm-4pm

Schedule

Resources

[IGV User Guide]

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!