Skip to Main Content

HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This workshop briefly introduces methods used in chromatin profiling experiments, including Transcription Factor / Histone ChIP-Seq and ATAC-Seq and also various data integration methods with gene expression data followed by a software demonstration using the HSLS-licensed Partek flow software.

Upon completing this class, you should be able to:

  • import ChIPSeq/ATACSeq reads from an NCBI GEO dataset
  • align the reads to a reference genome
  • identify, annotate and visualize the peaks from aligned ChIP-Seq /ATAC Seq data
  • identify enriched known/novel sequence motifs
  • integrate with gene expression data
  • find enriched gene sets and visualize the results

Target Audience

Experimental biologists seeking to analyze epigenomic data (ChIP-Seq/ATACseq) and also integrate with gene expression data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Workshop Materials

Software Registration



Data Download

Databases and Tools

Databases/Tools :




Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

[Software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.

If you used the Pitt-CRC server for CLC Genomics Workbench, then please also include the following text in the acknowledgments section for all publications, posters, and presentations: 

This research was supported in part by the University of Pittsburgh Center for Research Computing through the resources provided.