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RNA-Seq Analysis using CLC Genomics Workbench: Home


This hands-on workshop provides an introduction to RNA-seq analysis using the library-licensed CLC Genomics Workbench.

Participants will learn how to (1) align RNA-seq data to a reference genome, (2) calculate known genes and transcript expressions, & (3) perform differential expression analysis.

HSLS licensed software cited publications

Attribution Text

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: CLC Genomics Workbench software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.

Workshop Content

Massively parallel RNA sequencing, commonly known as RNA-seq, provides a more detailed picture of transcriptomes compared to microarray profiling. As Next-Generation Sequencing technologies are becoming faster and less expensive, RNA-seq is now the primary assay of choice for researchers investigating the abundance and diversity of RNA transcripts. Analysis of the large-scale data sets generated by a typical RNA-seq experiment is challenging as it demands access to powerful computers and researcher training to run sophisticated bioinformatics software packages. This workshop will teach how to analyze sample RNA-seq data using CLCbio Genomics Workbench software and the CLCbio Genomics Server installed at the PittCRC's HTC Cluster. The results will be further analyzed using BaseSpace Correlation Engine software.

Participants will gain hands-on experience to:

  • Download Illumina reads from NCBI Sequence Read Archive (SRA)/European Nucleotide Archive (ENA)
  • Align reads to the human reference genome
  • Estimate expression of known genes and transcripts
  • Perform differential expression analysis at the gene and transcript isoform level



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