Browse the manual

Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Data import and export
Reference Data Management
- QIAGEN Sets
SARS-CoV-2 workflows
- Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent)
- SARS-CoV-2 workflow output
  - Summary outputs
  - Sample specific outputs
QIAseq Sample Analysis
- Validate QIAseq Read Structure (beta)
  - Output from Validate QIAseq Read Structure (beta)
- The Analyze QIAseq Samples guide
- How to create a custom sample analysis workflow
  - Import QIAGEN Primers
- Create a custom Trim adapter list (optional)
- Unique Molecular Indexes (UMIs)
  - UMI group sizes
Targeted DNA
- The Identify QIAseq DNA Variants template workflows
- Create QIAseq DNA CNV Control Mapping workflows
  - Output from the Create QIAseq DNA CNV Control Samples workflow
- The Identify TMB Status template workflows
  - Output from the Identify TMB Status workflow
- The Detect QIAseq MSI Status template workflow
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation template workflow
- The Identify QIAseq DNA Ultra Somatic Variants template workflow
- The Calculate LOH template workflow
  - Output from the Calculate LOH workflow
- Targeted DNA tools detailed description
Targeted RNAscan
- The Detect QIAseq RNAscan Fusions template workflow
  - Output from the Detect QIAseq RNAscan Fusions workflow
- The Perform QIAseq RNA Fusion XP Analysis template workflows
  - Output from the Perform QIAseq RNA Fusion XP Analysis workflow
- Interpretation of fusion results
- Targeted RNAscan tools detailed description
Immune Repertoire
- Perform QIAseq Immune Repertoire Analysis template workflow
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- Immune Repertoire Expert Tools
Targeted Multimodal
- Perform QIAseq Multimodal Analysis (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis (Illumina)
- Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)
- Running the workflows in batch using Metadata
Targeted RNA
- The Quantify QIAseq RNA Expression template workflow
  - Output from the Quantify QIAseq RNA Expression workflow
- Targeted RNA tools detailed description
  - The Quantify QIAseq RNA tool
UPX 3' RNA
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' template workflow
  - Output from the Quantify QIAseq UPX 3' workflow
FastSelect RNA
- Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq FastSelect Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow
UPXome RNA
- Detect Wells
- Running the QIAseq UPXome workflows
- The Demultiplex QIAseq UPXome Reads workflow
- Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq UPXome Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT primer) workflow
Exome and xHYB
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Identify QIAseq xHYB Germline Variants
  - Identify QIAseq xHYB Germline Variants including Mitochondrial
- Identify QIAseq xHYB Somatic Variants
  - Identify QIAseq xHYB Somatic Variants including Mitochondrial
- Create QIAseq Exome CNV Control Mapping
  - Output from the Create QIAseq Exome CNV Control Mapping workflow
- Identify QIAseq Exome Causal Inherited Variants in Trio
  - Output from the Identify QIAseq Exome Causal Inherited Variants in Trio template workflow
Targeted Methyl
- The Detect QIAseq Methylation template workflows
  - Output from the Detect QIAseq Methylation workflow
- Targeted Methyl associated tools
QCI Interpret Integration
- Upload to QCI Interpret
- Prepare QCI Interpret Upload
- Upload Prepared QCI Interpret Report
QIAseq miRNA Analysis
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
  - Naming isomiRs
- QIAseq miRNA Differential Expression
- QIAseq miRNA Expert Tools
  - Create UMI Reads for miRNA
TruSight Oncology 500
- The Perform TSO500 DNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 DNA Analysis
- The Perform TSO500 RNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 RNA Analysis
QIAGEN GeneRead DNA Panel Analysis
- The QIAGEN GeneRead Panel Analysis workflow
  - Output from the QIAGEN GeneRead Panel Analysis
- Trim Primers and their Dimers from Mapping
Template 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)
- Hereditary Disease (WGS)
  - Filter Causal Variants (WGS-HD)
  - Identify Variants (WGS-HD)
Whole exome sequencing (WES)
- General Workflows (WES)
- Somatic Cancer (WES)
- Hereditary Disease (WES)
Targeted amplicon sequencing (TAS)
- General Workflows (TAS)
  - Annotate Variants (TAS)
  - Identify Known Variants in One Sample (TAS)
- Somatic Cancer (TAS)
- Hereditary Disease (TAS)
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
General tools
- Create Consensus Sequences from Variants
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
- Calculate HRD Score (beta)
- Target Region Coverage Analysis
  - Output from Target Region Coverage Analysis
Batching workflows
Legacy tools
- CNV and LOH Detection
Legacy workflows
- 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 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 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)
Appendices
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

Running the QIAseq UPXome workflows

All QIAseq UPXome workflows can be run from the Analyze QIAseq Samples guide or standalone from the toolbox. The main difference between these is the way reference data is applied. When running from the guide all reference data is pre-configured, whereas when running the workflow directly from the toolbox, the Barcodes reference table must be loaded or imported. The reference data element can either be

the list of barcodes generated from the Detect Wells tool described previously;
the reference data element from the QIAseq UPXome and FastSelect RNA hg38 QIAGEN sets located in the References manager.

All QIAseq UPXome workflows are designed to analyze all samples within an experiment without the need of batch functionality.

To run a workflow, first select the input reads, see figure 13.3.

Image upxomeselectreads
Figure 13.3: QIAseq UPXome workflows require multiplexed reads and analyze all samples within an experiment without the need of batch functionality.

Secondly select the wells used in the experiment. This is done in different ways depending on whether the workflow is run from the Analyze QIAseq Samples guide or the toolbox.

When running a workflow from the Analyze QIAseq Samples guide the well selection step looks like figure 13.4. The tool Detect Wells (see Detect Wells) can be used to get a list of wells detected using the first 10,000 reads of the input.

Figure 13.4: The wells used in the experiment should be selected in this step.
When running a workflow directly from the toolbox, first select the barcode table that will populate the dialog, see figure 13.5.

Figure 13.5: Load or import barcodes to have them visualized in the dialog.

Use Preview to identify relevant wells, click the "Preview (%)" column to sort by the number of reads per well, and Delete empty wells that are not of interest, see figure 13.6. In this way it is possible to tailor the number of elements generated to match the experimental design.

Figure 13.6: Use preview, then sort the barcodes and delete the unused wells.

Finally, specify the save location for the workflow output.