RNA-seq is a commonly used method for analyzing gene expression. This course will provide hands-on experience processing and analyzing high-throughput sequencing data, with an emphasis on RNA-seq.

By the end of the course students will be proficient with:

• Handling and processing high-throughput sequencing data
• High-throughput sequencing data quality control and filtering
• Alignment
• Differential gene expression analysis
• Data visualization

Lectures: Tuesdays and Thursdays, 10:00 - 11:50 am on ZOOM. You will receive a link via e-mail. The lectures will be very interactive, so attendance is encouraged. However, attendance is not mandatory. A recording of each lecture will be posted later in the day on Canvas, the same day of class.

Linux as a computational platform (DSCI 510) or a familiarity with UNIX/Linux and working from the command line.

Please see the course REQUIREMENTS for information on the computer you should bring to class, requesting SUMMIT access, and required software.

There is no textbook for this course. Reading assignments are papers describing the techniques used in the course.

We will have study sessions on Fridays from 1pm - 2pm. You can log in via the same zoom link as the course. You don't need to come to the study session with a question. You can just have the channel on as you work on your homework assignments. Feel free to benefit from questions others ask or join in on conversations or not. You can simply have the channel open in case a question pops up as you work through your assignments.

If you need to contact Dr. Nishimura, please use either e-mail or canvas.

Your grade for this course will be based on assignments, readings, lab notebook, and a final exam. The percentages are as follows:

• Assignments: 35 %
• Readings: 15 %
• Weekly quizzes (on canvas): 15 %
• Final project: 35 %

The calculation of the final letter grade will be made as follows:

• A 90 - 100%
• B 80 - 89.9%
• C 70 - 79.9%
• D 60 - 69.9%
• F below 60%

These ranges for a letter grade might be shifted a little lower, but will not be raised. We reserve the right to distribute + or - grades.

Late assignments will be accepted if you make arrangements with the instructor 24 hrs before the due date. You will be given 48 additional hours to complete the assignment.

Assignments - There will be 6 assignments worth 7 pts each. Your lowest assignment score will be dropped for a total of 35 possible points.

Readings – Three will be 6 readings worth 3 pts each. Your lowest reading score will be dropped for a total of 15 possible points.

Quizzes – will be available on canvas between the close of Thursday's class and the beginning of Tuesday's class.

You are expected to be familiar with the Student Code of Conduct. This course will adhere to the CSU Academic Integrity Policy. At a minimum, violations will result in a grading penalty in this course and a report to the Office of Conflict Resolution and Student Conduct Services.

Colorado State University has clear Principles of Community. We each have the responsibility to uphold these values as we interact with one another and learn.