Coronavirus information for Feinberg.

Skip to main content

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.

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 working with remote servers, operating using only the command line, the various tools available for RNA-seq analysis, quality control of sequence reads, alignment, gene quantification, differential expression, pathway analysis and data interpretation.

Please contact Matt Schipma if you have any questions. 


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 one to three hours per week, including class time and assigned exercises.  


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

Watch a video recording of the Oct. 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

Watch a video recording of the Sept. 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

Watch a video recording of the Sept. 20, 2018, session.

Session 4: Alignment Strategies

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

Watch a video recording of the Sept. 27, 2018, session.

Session 5: Quantification

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

Watch a video recording of the Oct. 11, 2018, session.

Session 6: Advanced Analysis

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

Watch a video recording of the Oct. 18, 2018, session.