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RNA-Seq Analysis using Galaxy: Home

Overview

Galaxy is a web-based platform for the biologist to perform Next-Generation Sequence analysis using open source bioinformatics software.  It does not require programming or Linux command line experience.  An institutional galaxy server is available for the Pitt research community through the Center for Research Computing.

This hands-on workshop teaches the basics of Galaxy including (1) the interface navigation and interaction and (2) how to perform a reference-based RNA-seq data analysis using open source bioinformatics software packages such as HISAT, FeatureCounts and DESeq2. 

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 Galaxy software installed at the Pitt CRC HPC. 

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

 

Key References

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