Northwestern University Feinberg School of Medicine

Center for Genetic Medicine

RNA-Seq Data Analysis: Bioinformatics Seminar

The Center for Genetic Medicine hosts a biannual bioinformatics seminar. The course is led by Matthew Schipma, PhD, Associate Director of the NUSeq Core Facility and Research Assistant Professor of Biochemistry and Molecular Genetics.

Schipma initially developed the course with former Feinberg faculty member Ann Harris, PhD at the Stanley Manne Children’s Research Institute. We aim to expand the program on the Chicago campus in order to develop this increasingly-critical skill set among students, staff, and faculty.  

Course Objectives

In this course, students will learn the basic concepts of RNA-seq including principles and experimental design. Students will also develop hands-on experience in:


Matthew Schipma has over 10 years of bioinformatics experience. He holds a PhD in Biochemistry and an MS in Computer Science. He worked as a post-doctoral appointee at Argonne National Laboratory writing statistical programs to automate the analysis of biochips. Schipma then worked for Integrated Genomics Inc, where he worked in microbial genomics, DNA sequencing and assembly.  Since 2010, he has been at Northwestern University in the Center for Genetic Medicine providing bioinformatics analysis for next-generation sequencing projects.


No prior experience with RNA-Seq Data Analysis is required; the course is designed as an introduction. Attendees will need to bring a laptop to each seminar. Instructions for installing and using the required software – Xming and PuTTY – will be covered during the first seminar session. The time commitment for the seminar will be 1-3 hours per week, including class time and assigned exercises.  


The topics covered in each session are outlined below.

Session 1: Overview and Connecting to Server

  • Overview of course
  • Introduction to analysis hardware and software
  • How to connect with Macbook
  • How to connect with PC

Videorecording of October 4, 2018 session

Session 2: Introduction to the Command Line Interface

  • File management
  • Navigating file structure
  • Creating directories
  • Deleting files/directories
  • Text editors
  • PATH and bash_profile
  • Symbolic links

Videorecording of September 13, 2018 session

Session 3: Considerations of Experimental Design

  • Library prep
  • mRNA vs. total RNA
  • strand-specificity
  • Depth of coverage
  • Number of replicates
  • Collection of RNA
  • ERCC

Videorecording of September 20, 2018 session

Session 4: Alignment Strategies

  • Cleaning the reads
  • Quality control
  • Genome vs. transcriptome alignment
  • TopHat
  • STAR

Videorecording of September 27, 2018 session

Session 5: Quantification

  • Gene expression or transcript/isoform expression
  • RPKM vs. read counts
  • Cufflinks vs. DESeq(2)
  • RSEM

Session 6: Advanced Analysis

  • Pathway analysis
  • Free or commercial
  • Promoter analysis
  • Gene networks
  • Visualization
  • Heat maps
  • Scatterplots


Please contact Matt Schipma if you have any questions regarding the seminar.