Partek Flow software workshop on campus-March 10, 2016

To honor requests from Researchers on campus, Becker Library recently purchased a Partek Flow group license for the WUSM community. The WUSM Partek Flow license is installed on the WUSM Center for High Performance Computing cluster and managed by Becker Library. Partek Flow is a web-based software application with an easy-to-use graphical interface designed specifically for the analysis of next generation sequencing data including RNA, small RNA, and DNA sequencing data.

Partek provides free onsite training sessions at WUSM each year as part of our group license. To kick off the new Flow license, a Field Application Scientist from Partek will lead a full day Partek Flow hands-on workshop, on March 10, 2016 for the analysis of RNA-Seq  and DNA-Seq data. This workshop will run from 9:30am-3:30pm in the computer classroom in Farrell Learning and Teaching Center (FLTC Room 602), with the following agenda:

Morning session (Hands On: Analysis on RNA-Seq Data): The morning session will start with a hands-on session to learn how to analyze RNA-Seq data. Topics will include how to use statistical tests to identify differentially expressed transcripts and alternative spliced genes among sample groups, how to generate a list of genes of interest and identify high level biological trends using Gene Ontology.

  • Import data (fastq, bam, text format)
  • Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC)
  • Trim bases
  • Alignment
  • Gene/transcript abundance estimate (E/M)
  • Differential expression detection (GSA, ANOVA)
  • Filter gene list
  • GO Enrichment Analysis
  • Visualization ( Quality score distribution, Base composition, PCA scatterplot, Dotplot, Volcano plot, Hierarchical clustering, Chromosome view)

Afternoon Session (Demo: Integration of RNA-Seq with Microarray Gene Expression Data; DNA-Seq Data Analysis Pipeline; Q&A): The afternoon session will start with the integration of RNA-Seq and Gene Expression Microarray data in Partek Flow, followed by a live demo on the DNA-Seq Data Analysis pipeline and end with a Q&A session.

This training is free and open to the Washington University community. Registration is required. To register for the workshop, please complete the workshop registration form.

If you have questions, contact Maze Ndonwi at ndonwimaze@wustl.edu or 314 362 4737.