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.
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
- gene quantification
- differential expression
- pathway analysis
- data interpretation
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
Videorecording of October 4, 2018 session
Session 2: Introduction to the Command Line Interface
Videorecording of September 13, 2018 session
Session 3: Considerations of Experimental Design
Session 4: Alignment Strategies
Session 5: Quantification
Session 6: Advanced Analysis
Please contact Matt Schipma if you have any questions regarding the seminar.