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RNA-seq Course Description

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

Time and Place

Lectures: Tuesdays and Thursdays, 10:00 - 11:50 am in Biology 134.


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 assignment are papers describing the techniques used in the course.


We will be using Canvas Discussions for class-wide communications.


Office Office Hours
Dr. Erin Nishimura MRB 239 by appointment
Dr. David King MRB 227 guest lecturer


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 %
  • Lab Notebook: 25 %
  • Final exam: 25 %

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.

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.


Erin's section will have a 5 minute quiz at the beginning of each class. These are not graded.


You are expected to be familiar with the CSU 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.

rnaseq_syllabus.txt · Last modified: 2018/11/14 09:11 by erin