Product manuals
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Introduction
The concept of Biomedical Genomics Analysis
System requirements
Contact information
Data import and export
BGI/MGI Sequencing Import
Illumina Custom Reads
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
The Analyze QIAseq Samples guide
Import your reads
Start a QIAseq sample analysis
Guide Upload to QCI Interpret
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 ready-to-use workflows
Output from the Identify QIAseq DNA Variants workflows
Quality Control for the Identify QIAseq DNA Variants workflow
Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina)
Output from the Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina) workflow
QIAseq DNA Pro workflows
Create QIAseq DNA CNV Control Mapping workflows
Output from the Create QIAseq DNA CNV Control Samples workflow
The Identify TMB Status ready-to-use workflows
Output from the Identify TMB Status workflow
The Detect QIAseq MSI Status ready-to-use workflow
Output of the Detect QIAseq MSI Status workflow
Detect MSI Status with Baseline Creation ready-to-use workflow
Targeted DNA tools detailed description
Annotate Structural Variants
Convert Annotation Track Coordinates
Calculate TMB Score
Detect MSI Status
Extract Reads Matching Primers
Generate MSI Baseline
Refine Read Mapping
Remove and Annotate with Unique Molecular Index
Calculate Unique Molecular Index Groups
Create UMI Reads from Grouped Reads
Create UMI Reads from Reads
Remove Ligation Artifacts
Trim Primers of Mapped Reads
Identify Mispriming Events
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
The Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows
Output from the Perform QIAseq RNA Fusion XP Analysis workflow
Interpretation of fusion results
Targeted RNAscan tools detailed description
Detect and Refine Fusion Genes
Annotate Fusions with Known Fusion Information
QC for RNAscan Panels
Annotate RNA Variants
Import Known Fusion Information Track
Immune Repertoire
Perform QIAseq Immune Repertoire Analysis ready-to-use workflow
Output from the Perform QIAseq Immune Repertoire Analysis workflow
QIAseq Immune Repertoire Expert Tools
Import VDJtools Clonotypes
Immune Repertoire Analysis
Compare Immune Repertoires
Targeted Multimodal
Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow
Output from the Perform QIAseq Multimodal Analysis (Illumina)
Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) ready-to-use 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 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
UPXome
Detect Wells
The Quantify QIAseq UPX v2 ready-to-use workflow
Output from the Quantify QIAseq UPX v2 workflow
Exome
Identify QIAseq Exome Germline Variants
Output from the Identify QIAseq Exome Germline Variants ready-to-use workflow
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 ready-to-use workflow
Targeted Methyl
The Detect QIAseq Methylation ready-to-use workflows
Output from the Detect QIAseq Methylation workflow
Targeted Methyl associated tools
Finding differentially methylated regions
Create Methylation Level Heat Map
Predict Methylation Profile (beta)
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
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)
Annotate Variants with Effect Scores (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
General tools
Create Consensus Sequences from Variants
CNV and LOH Detection
Region-level CNV track (Region CNVs)
Target-level CNV track (Target CNVs)
Gene-level annotation track (Gene CNVs)
Loss-of-heterozygosity track
CNV results report
CNV algorithm report
Structural Variant Caller
Output from the Structural Variant Caller
Calculate LOH and HRD (beta)
Target Region Coverage Analysis
Output from Target Region Coverage Analysis
Batching workflows
Legacy tools
Detect Fusion Genes
Refine Fusion Genes
Appendices
Install and uninstall plugins
Installation of plugins
Uninstalling plugins
Bibliography
Somatic Cancer (WES)
Subsections
Filter Somatic Variants (WES)
Identify Somatic Variants from Tumor Normal Pair (WES)
Identify Variants (WES)
Identify and Annotate Variants (WES)