Downstream processing of RNA-Seq data in GenePattern

Trainer Barbara Hill Meyers and Michael Reich
BITS Courses TRAINING AT VIB

Goal

  • - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA...
  • - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers
  • - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place

Summary

The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists.
  • 1. Running Analyses in GenePattern
  • 2. Clustering
  • 3. Prediction and Clasification
  • 4. Working with analysis workflows: GenePattern pipelines
  • 5. Working with Samples and Features
  • 6. The GenePattern Notebook environment
  • 7. Related tools: IGV, GSEA
  • 8. Open Q&A

The data files, slides and exercises will be made available after the workshop.

 

Prerequisites

None

Schedule

Training material

Exercises on using GenePattern and IGV

Slides

Links

None

Scientific topics RNA-Seq, Data managment, Gene prediction
Target audience Life Science Researchers, PhD students, post-docs