CLC Genomics Workbench 12 and Ingenuity Variant Analysis (IVA) & Ingenuity Pathway Analysis (IPA) Training

Course date: 29 April 2019 - 30 April 2019
Location: Erasmus MC, Ee 15.28

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(1st day)

One-day hands-on training workhop by the team from Qiagen about the CLC Genomics Workbench 12  and Ingenuity Variant Analysis (IVA).

This hands-on training workshop will introduce users to the CLC Genomics Workbench 12 (https://www.qiagenbioinformatics.com/products/clc-genomics-workbench) for the fast and efficient processing and visualisation of Human NGS data, and to Ingenuity Variant Analysis (https://www.qiagenbioinformatics.com/products/ingenuity-variant-analysis/) for the identification, prioritisation and biological interpretation of DNA Variants. The case study will cover the basics of data visualisation, QC, the creation of user-constructed workflows, and the identification of variants from targeted human DNA resequencing using the Workbench. The biological significance of the variants will then be interpreted using Ingenuity Variant Analysis which will allow users to additionally annotate, filter and prioritise variants based on their biological relevance.

Topics

Introduction to QIAGEN Sample to Insight, CLC Genomics Workbench 12 and Ingenuity Variant Analysis

  • Getting Started with the CLC Genomics Workbench 12

  • Loading human fastq data and performing QC

  • Alignment of reads to a Reference genome, coverage and QC

  • Variant Calling and variant-level annotation

  • Workflows for different data types

  • Integrating the Workbench with Ingenuity Variant Analysis

  • Creating an Analysis of multiple samples in Variant Analysis

  • Biological interpretation of variants

  • Refining filters, refining the analysis

  • Advanced Analysis Tips and Tricks
 (2nd Day)
 
 
Ingenuity Pathway Analysis (IPA) Training

This hands-on training workshop will introduce new users to Ingenuity Pathway Analysis (https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/) for the biological interpretation of ‘omic data, and provide additional information for inexperienced users of the system. The training will use an RNA-Seq data set as a case study. For example, the transcriptional changes observed in hepatocellular carcinomas in comparison to paired normal liver tissue. The course will also highlight the considerations when analysing and integrating other data types such as proteomics or metabolomics data, and will touch on the analysis of miRNA.

Course Topics:

  • Introduction to QIAGEN Sample to Insight and Ingenuity Pathway Analysis (IPA)
  • Uploading data and running a Core Analysis
  • Interpreting a Core Analysis
    o Canonical Pathways Analysis
    o Upstream Regulator Analysis
    o Downstream Effect Analysis
    o Molecular Network Analysis
  • Search & Pathway Building; Search & Explore case study
  • Comparison Analysis & Analysis Match
  • Sharing & Collaboration
  • Best Practice Tips & Tricks
  • Overview of other IPA analysis tools
 You can register for each single day, or for both days.
 
 Teachers: Kim Madsen & André Koper, QUIAGEN
 
 
 
 

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