During the tutorial sessions of this class all students will perform the basic data analysis of three NGS Workflows including RNA-Seq, ChIP-Seq and VAR-Seq. In addition, every student will work in a group of 3-5 students on a Challenge Project addressing a specific data analysis task within one of the three NGS Workflows. Students will also present a scientific paper closely related to their challenge topic (see here). To facilitate teamwork among group members, each course project will be assigned a private GitHub repository (see here).

The results of the Challenge Projects will be presented by each student group during the last week of the course (see Slideshow Template here). In addition, each student will write a detailed analysis report of the assigned course project. This report needs to include all analysis steps of the corresponding NGS Workflow (e.g. full RNA-Seq analysis) as well as the code and results of the Challenge Project. The final project reports should be written in R Markdown. A basic tutorial on R Markdown is available here. Both the R Markdown script (.Rmd) along with the rendered HTML or PDF report will be submitted to each student’s private GitHub repository. All helper code used for the challenge project needs to be organized as well documented R functions in each project’s *_Fct.R script. The expected structure of the final project report is outlined below.

The reports should be submitted to each student’s private GitHub repository that was used to submit the homework assignments. For the report each student should create in this repository a new directory named ProjectReport and include in it the following files:

  • .Rmd source script of project report
  • Report rendered from .Rmd source in HTML or PDF format
  • ._Fct.R file containing all helper functions used for challenge project
  • Submission Deadline for reports: 6:00 PM, June 12th, 2018

Structure of final project report

  1. Abstract
  2. Introduction
  3. Methods
    • Short description of methods used by NGS workflow
    • Detailed description of methods used for challenge project
  4. Results and Discussion
    • Includes all components of NGS workflow as well as challenge project
  5. Conclusions
  6. Acknowledgments
  7. References
  8. Supplement (optional)