Workshop – Analyzing Illumina RNA-­seq Data with the CRI

Title – Analyzing Illumina RNA-­seq Data with the CRI

Instructor – Elizabeth Bartom, PhD and Lei Huang, PhD

Location – Biological Sciences Learning Center – Room 018 (basement)

Date & Time – February 25, 2013 9am-12pm

Register – Register Here

RNA-seq is a revolutionary approach to transcriptome profiling that uses the next-generation sequencing technologies. It provides more accurate measurement of the expression levels of transcripts and their isoforms compared to other methods including microarrays. In this tutorial, we will learn to use the CRI’s RNA-Seq pipeline (available on brdfgate server, BIOS HPC cluster, and CRI Galaxy) to analyze Illumina RNA sequencing data. The analysis will be performed in four steps :

  • Step 1: Assess the sequencing data quality using FastQC
  • Step 2: Align the short reads to the human genome using Tophat
  • Step 3: Analyze expression using Cufflinks
  • Step 4: Collate results with in-house scripts

(find out more…)

The Center for Research Informatics (CRI) provides computational resources and expertise in biomedical informatics for researchers in the Biological Sciences Division (BSD) of the University of Chicago. This workshop is part of a series of monthly training events focusing on using University of Chicago’s computational resources to analyze Next-Generation Sequencing and Microarray data.

As a bioinformatics core, we are actively improving our pipelines and expanding pipeline functions. The tutorials will be updated in a timely manner but may not reflect the newest updates of the pipelines. Stay tuned with us for the latest pipeline release.

If you have any questions, comments, or suggestions, feel free to contact our core at or one of our bioinformaticians.