• Manuals

Browse the manual

• Introduction
  • The concept of Biomedical Genomics Analysis
  • System requirements
  • Contact information
• QIAseq Panel Analysis
  • Data management
  • The Analyze QIAseq Panels guide
    • Import your reads
    • Start a QIAseq panel analysis
    • Upload to QCI Interpret
  • How to create a custom panel analysis workflow
    • Import QIAGEN Primers
  • Create a custom Trim adapter list (optional)
• Targeted DNA
  • The Identify QIAseq DNA Variants ready-to-use workflows
    • Output from the Identify QIAseq DNA Variants workflow
    • Quality Control for the Identify QIAseq DNA Variants workflow
  • The Identify TMB Status ready-to-use workflows
    • Output from the Identify TMB Status workflow
  • The Detect QIAseq MSI Status (beta) ready-to-use workflow
    • Output of the Detect QIAseq MSI Status workflow
  • Targeted DNA tools detailed description
    • Calculate TMB Score
    • Detect MSI Status (beta)
    • Generate MSI Baseline (beta)
    • Remove and Annotate with Unique Molecular Index
    • Calculate Unique Molecular Index Groups
    • Create UMI Reads
    • Remove Ligation Artifacts
    • Trim Primers of Mapped Reads
    • Annotate Variants with Unique Molecular Index Info
    • Prepare Guidance Variant Track
    • Import Gene-Pseudogene Table
• Targeted RNAscan
  • The Detect QIAseq RNAscan Fusions ready-to-use workflow
    • Output from the Detect QIAseq RNAscan Fusions workflow
    • Interpretation of the Detect QIAseq RNAscan Fusions results
  • Targeted RNAscan tools detailed description
    • Detect Fusion Genes
    • Refine Fusion Genes
    • Annotate Fusions with Known Fusion Information
    • QC for RNAscan Panels
    • Import Known Fusion Information Track
• Targeted RNA
  • The Quantify QIAseq RNA Expression ready-to-use workflow
    • Output from the Quantify QIAseq RNA Expression workflow
  • Targeted RNA tools detailed description
    • The Quantify QIAseq RNA tool
• UPX 3'
  • Demultiplex QIAseq UPX 3' reads
  • The Quantify QIAseq UPX 3' ready-to-use workflow
    • Output from the Quantify QIAseq UPX 3' workflow
• Targeted Methyl
  • The Detect QIAseq Methylation ready-to-use workflow
    • Output from the Detect QIAseq Methylation workflow
    • Finding differentially methylated regions
• QCI Interpret Integration
  • Configuration of the Upload to QCI Interpret tool
  • The Upload to QCI Interpret tool
• QIAseq miRNA Analysis
  • QIAseq miRNA Quantification
    • QIAseq miRNA Quantification outputs
  • QIAseq miRNA Differential Expression
  • QIAseq miRNA Expert Tools
    • Create UMI Reads for miRNA
    • Quantify miRNA
    • Annotate with RNAcentral Accession Numbers
    • Create Combined miRNA Report
• QIAGEN GeneRead DNA Panel Analysis
  • The QIAGEN GeneRead Panel Analysis workflow
    • Output from the QIAGEN GeneRead Panel Analysis
  • Trim Primers and their Dimers of Mapped Reads
• Ready-to-use workflows descriptions and guidelines
  • General Workflow
  • Somatic Cancer
  • Hereditary Disease
• Getting started
  • Import sequencing data
  • Prepare Raw Data
• Whole genome sequencing (WGS)
  • General Workflows (WGS)
    • Annotate Variants (WGS)
    • Identify Known Variants in One Sample (WGS)
  • Somatic Cancer (WGS)
    • Filter Somatic Variants (WGS)
    • Identify Somatic Variants from Tumor Normal Pair (WGS)
    • Identify Variants (WGS)
  • Hereditary Disease (WGS)
    • Filter Causal Variants (WGS-HD)
    • Identify Causal Inherited Variants in Family of Four (WGS)
    • Identify Causal Inherited Variants in Trio (WGS)
    • Identify Rare Disease Causing Mutations in Family of Four (WGS)
    • Identify Rare Disease Causing Mutations in Trio (WGS)
    • Identify Variants (WGS-HD)
• Whole exome sequencing (WES)
  • General Workflows (WES)
    • Annotate Variants (WES)
    • Identify Known Variants in One Sample (WES)
  • Somatic Cancer (WES)
    • Filter Somatic Variants (WES)
    • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Identify Variants (WES)
    • Identify and Annotate Variants (WES)
  • Hereditary Disease (WES)
    • Filter Causal Variants (WES-HD)
    • Identify Causal Inherited Variants in Family of Four (WES)
    • Identify Causal Inherited Variants in Trio (WES)
    • Identify Rare Disease Causing Mutations in Family of Four (WES)
    • Identify Rare Disease Causing Mutations in Trio (WES)
    • Identify Variants (WES-HD)
    • Identify and Annotate Variants (WES-HD)
• Targeted amplicon sequencing (TAS)
  • General Workflows (TAS)
    • Annotate Variants (TAS)
    • Identify Known Variants in One Sample (TAS)
  • Somatic Cancer (TAS)
    • Filter Somatic Variants (TAS)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • Identify Causal Inherited Variants in Family of Four (TAS)
    • Identify Causal Inherited Variants in Trio (TAS)
    • Identify Rare Disease Causing Mutations in Family of Four (TAS)
    • Identify Rare Disease Causing Mutations in Trio (TAS)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• Whole Transcriptome Sequencing (WTS)
  • Annotate Variants (WTS)
  • Compare Variants in DNA and RNA
  • Identify Candidate Variants and Genes from Tumor Normal Pair
  • Identify Variants and Add Expression Values
  • Identify and Annotate Differentially Expressed Genes and Pathways
• Batching workflows
• Appendices
  • Legacy tools
    • Trim Primers of Mapped Single Reads
    • Trim Primers of Mapped Paired End Reads
  • Install and uninstall plugins
    • Install
    • Uninstall
• Bibliography

Configuration of the Upload to QCI Interpret tool

The workbench can be configured to allow seamless upload of analysis results to QCI Interpret. Configuration of the Upload to QCI Interpret tool depends on having an active QCI Interpret subscription (not a trial license), and a QCI Interpret account with API license privileges.

If an API user account has not been set up for you, please contact support-license@qiagen.com. In your email, ask to have an API enabled QCI Interpret account set up for the Biomedical Genomics Analysis plugin integration. The license team can then send you your API Key ID and API Key Secret.

To retrieve yourself your user's API Key ID and an API Key Secret number, log in to QCI Interpret using the following links:

• QCI Interpret US: https://apps.ingenuity.com/qcibridge
• QCI Interpret UK: https://apps.qiagenbioinformatics.eu/qcibridge
• QCI Interpret China: https://variants.qiagenbioinformatics.cn/qcibridge

You can then access the API Explorer (as seen in figure 8.1 and figure 8.2):

Figure 1: Accessing the QCI Interpret API Explorer.

Figure 2: Finding the API Key Id and API Key Secret in the API Explorer.

Once you have the necessary information, you can start using the Upload to QCI Interpret tool.

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