In this course, students will analyze eukaryotic High Throughput Sequencing (aka "Next Generation Sequencing") data. Students will carry out a research project in small groups, have weekly lab meetings, and write lab reports.

Prequisites

Students taking this section must have permission of instructor.

Under certain circumstances, the instructor may have to alter course requirements, assignment deadlines, and grading procedures; and the university may have to alter the academic calendar.

Each project will use real HTS data. Student form teams and pick one project during Week 3. Students will spend the rest of the semester analyzing this data set.

For each project, there may be trees of primary, secondary, and tertiary analysis steps, which are dependent on each other. For example, any Secondary Analysis will be dependent upon having a Primary Analysis that was completed correctly. Completion of more than three levels of analysis can result in bonus points! Be sure to ask the instructor well in advance if you wish to carry out the additional work to verify that it is appropriate.

Participation for each step of analysis will be graded for elements such as completeness, choice of analysis method, appropriate parameter choice, demonstration of active participation, and regular online communications through the myCourses Discussion groups. Individual participation, including full participation in all class sessions, will also be observed and incorporated.

Readings are due before the lecture meetings of that week. These readings are intended both to acclimate you to the topic of the week, and serve as discussion for that week. All papers should be available through myCourses, although some are linked out. In no case should you have to pay for any articles!

Over the semester, students must submit individual lab reports for 10 out of the 12 available weeks, counting the project choice. Reports must be one-half to two single spaced pages for undergraduates, or one to two pages for graduate students, submitted to the correct myCourses dropbox before the next week's Friday meeting. Reports must include the following elements:

• What was accomplished since the previous report, especially regarding the previous report's future goals. (Not necessary for first report.)
• Methods used, including commands used with parameters
• What problems you encountered
• Goals for the coming week

A final paper written by the group, explaining your work, in a typical journal format, is due submitted to the myCourses dropbox before the end of the last day of classes (Monday, April 29th, 11:59pm). No late papers will be accepted.

Part of a draft, written by the group, is due during Weeks 13 through 15 on the following schedule. Drafts must be submitted to the appropriate myCourses DropBox before Thursday workshop. Each draft is worth 1% of your final grade, for a total of 3%. No late drafts will be accepted for a grade. For drafts, color your individual text in a color unique to you among your group. You must use MS Word, LibreOffice, or OpenOffice. Word is available from the COS computer labs and the others are free. Be sure to include one comment at the start of the draft with your full name so that your revision color can be identified.

• Week 13 - Outline of the paper.
• Week 14 - Draft of half of the text.
• Week 15 - Draft of the rest of the paper.

• 30-50 pages
• Minimum of 15 primary sources.
• No more than half figures/tables. The rest must be prose.
• 8.5" x 11" paper-size
• double-spaced
• Citations do not count for or against the page requirements.
• MS Word 2016 or later, LibreOffice, or OpenOffice. Do not use Google Docs which creates formatting issues.
• 10 or 12 point Calibri or Times New Roman font.
• Exactly 1" margins.
• No more than one page of direct quotes in total.
• Proper spelling, grammar, and style.
• Standard scientific sections (Introduction, Materials and Methods, Results, Discussion, References).

Recording policy

Unless written permission is granted by the faculty member, or a specific accommodation has been approved by the Disability Services Office, students are prohibited from recording lectures or presentations.