tv.qiagenbioinformatics.com

Single-cell RNA-seq analysis made easy - February 24

Wed, 28 Jan 2026 21:53:39 GMT

Single-cell gene expression analysis starting from either FASTQ or expression data is now supported by QIAGEN CLC Genomics Workbench Premium, the scalable cross-platform desktop software for NGS data analysis. In this webinar, we will re-analyze data from a study on transcriptional profiling of the mouse heart (Skelly et al., 2018), starting from FASTQ and ending with detecting sexually dimorphic genes within different cell types.

Reference: Skelly, Daniel A., et al. (2018) Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell reports 22.3: 600-610.

Topics covered:
• Introduction to the QIAGEN CLC Genomics Workbench
• Generation of t-SNE and UMAP plots, starting from raw FASTQ read files
• Automated annotation of cell types using QIAGEN’s cell type classifier
• Detection of differentially expressed genes in different cell types in a case vs. control setting

ChIP-seq, Histone-seq and Methyl-seq analysis using CLC Genomics Workbench

Thu, 26 Jun 2025 22:42:47 GMT

This training will focus on how a user can analyze their epigenomics data using QIAGEN CLC Genomics Workbench.

Specifically, the trainer will cover how to

• Import the raw sequencing data

• Download or import reference, metadata and other needed files

• Mapping reads to a reference genome

• Calling and visualizing peaks

• Export graphical and tabular results

In addition, per registrant feedback and the trainer discretion additional topics such as customizing the workflow, how to send data to Ingenuity Pathway Analysis and more may be covered.

De novo assembly, BLAST and genome finishing using CLC Genomics Workbench

Wed, 18 Jun 2025 15:20:48 GMT

This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.

Participants will learn the following:

o Download and install needed plugins.

o Import data required for the analysis.

o Run the de novo assembly workflow.

o For long reads, improve a de novo assembly by polishing with short, high-quality reads.

o Map reads to a reference and visualize an assembly.

o For long reads, correct raw long reads for further analysis.

o Use BLAST to investigate the contigs.

o Analyze and assemble contigs through Genome Finishing tools.

RNA-seq analysis for long reads

Tue, 10 Jun 2025 16:43:30 GMT

This training will focus on how a user can analyze their long reads data using QIAGEN CLC Genomics Workbench.

Specifically, the trainer will cover how to

• Import the long reads data

• Download or import reference, metadata and other needed files

• Process such data and generate downstream RNA-seq outputs

• Export high resolution graphics and tables

In addition, per registrant feedback and trainer discretion additional topics such as customizing the workflow, how to send data to Ingenuity Pathway Analysis, Sankey plot and more may be covered.

Shotgun metagenomics taxonomic profiling using QIAGEN CLC Genomics Workbench

Tue, 03 Jun 2025 15:22:01 GMT

The QIAGEN CLC Microbial Genomics Module provides tools and workflows for many bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training focuses on whole shotgun metagenomics taxonomic profiling. Specifically, we’ll cover:

• An overview of the different tools within QIAGEN CLC Microbial Genomics Module and the research areas supported

• Taxonomic profiling

• Importing data

• Utilization of metadata

• Downloading and managing references

• Taxonomic profiling workflow (analytical pipeline)

• Downstream processing of abundance tables

• Creating and exporting high-quality graphics

Multimodal panels analysis using QIAGEN CLC Genomics Workbench

Thu, 15 May 2025 10:53:39 GMT

This training will go over how QIAGEN CLC Genomics Workbench can be used to analyze Multimodal Panels data.

Trainer will cover

• How to import your data and metadata and download reference and other needed files

• How to use workflow and customize it

• How to visualize and export the results

DNA-seq (whole genome, whole exome, DNA-panel) analyses using QIAGEN CLC...

Thu, 24 Apr 2025 15:29:42 GMT

In this training, we’ll go over how to easily perform DNA-seq (specifically whole genome, whole exome, DNA-panel and similar) analyses easily and effectively using QIAGEN CLC Genomics Workbench.

Together, we’ll explore:

• Read mapping

• Variant calling (SNPs, mutations, Indels and more)

• Annotations and filters

• Genome browser view

Please bring any questions you may have, and we will answer them during this training.

Isolate Typing, Strain Identification and Antimicrobial Resistance Analyses...

Tue, 22 Apr 2025 08:00:36 GMT

QIAGEN CLC Genomics Workbench provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization through SNP and K-mer trees using NGS data, and antimicrobial resistance characterization. CLC Genomics Workbench is widely used for analyses of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

Topics covered in this webinar include:

I. Overview of different tools within MGM application and research areas supported

II. II. Focused review of isolate typing and characterization

III. a. How to import data

IV. b. Using metadata

V. c. Downloading and managing references, including databases of isolates/resistances/MLST

VI. d. Walkthrough of the "Type a Known Species" workflow and review of details for each isolate

VII. e. Creating SNP profiles to specific reference

VIII. f. Generate a SNP tree for isolate comparison

IX. g. Export tabular and high-quality graphical outputs in wide range of file formats

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Wed, 16 Apr 2025 01:54:25 GMT

Recently we have received some requests from CLC users (as well as CLC RNA-seq certification participants) to go over workflow construction and customization using CLC Genomics Workbench. Accordingly, we are hosting this training. The term workflow refers to bioinformatics secondary analysis pipelines such as DNA-seq, RNA-seq, OTU clustering, de novo assembly and more offered by CLC Genomics Workbench.

In this training, the trainer will go over

• The basics of workflow construction

• How to visualize different steps of the workflow and customize different settings

• How to edit workflows (add/remove steps, lock/unlock parameters and more)

• How to share workflows

• How to install workflows

• Other workflow related topics

Overlaying Expression Data onto UMAP Plots using the Single Cell Analysis...

Thu, 03 Apr 2025 12:50:28 GMT

In this video, we show how to color cells based on the expression of genes of interest in a UMAP. We also demonstrate how to examine expression values from the plot in a selected group of cells.

Recent training webinar and tutorial that includes UMAP plot generation from single-cell data:

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Tutorial: Perform Single-Cell RNA Expression and Velocity Analysis

Finding the Perfect CLC Tool for your Workflow

Thu, 03 Apr 2025 12:49:05 GMT

Here are some quick tips on locating tools in CLC Genomics Workbench version 25+

Visualizing Spatial Transcriptomics Data in CLC Genomics Workbench

Thu, 03 Apr 2025 12:47:47 GMT

How to import and visualize spatial transcriptomics data in CLC

Installing CLC Network License manager and Downloading Network Licenses on...

Thu, 03 Apr 2025 12:46:31 GMT

How to install the CLC network license manager, network licenses, and CLC Genomics Workbench on Windows

Convenient Way To Launch Analysis Tools from UMAP Plots in the Single Cell...

Thu, 03 Apr 2025 12:45:27 GMT

In this video, we demonstrate the different tools that can be launched directly from the UMAP plot with a simple right-click.

Recent training webinar and tutorial that includes UMAP plot generation from single-cell data:

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Tutorial: Perform Single-Cell RNA Expression and Velocity Analysis

Importing Single Cell Data into CLC Genomics Workbench

Thu, 03 Apr 2025 12:44:12 GMT

Single cell expression matrices can be imported into CLC manually using the import single cell matrix tool or they can be imported automatically using workflows. https://resources.qiagenbioinformatics.com/manuals/clcsinglecellanalysis/current/index.php?manual=Import_Expression_Matrix.html

Precise Workflow Path Control using Branching Elements

Thu, 03 Apr 2025 12:42:35 GMT

Direct outputs through a workflow based on sequence count, coverage, and sample quality using branching elements https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Branching_elements.html

Wrapping external applications into QIAGEN CLC Genomics Workbench

Thu, 27 Mar 2025 09:48:58 GMT

QIAGEN’s CLC bioinformatics software portfolio provides user-friendly and intuitive solutions that run on any platform. This helps scientists to focus on the biology of their research without requiring them to write code, or compile and run software from the command line.

At QIAGEN we understand, however, that no single piece of software can meet the needs of every bioinformatics challenge. Sometimes, you need to supplement standard pipelines with your own scripts, open-source tools or third party applications from the command-line.

Accordingly, this training will go over:

• A quick introduction to CLC Genomics Workbench

• Wrapping an external application into the CLC environment

• Running external application alongside CLC tools and exporting results.

RNA-seq data analysis using QIAGEN CLC Genomics Workbench

Tue, 25 Mar 2025 12:35:35 GMT

For RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata and how to download references

• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, sankey plot and others

• Easily customize RNA-seq workflows • Export publication-quality graphics, tables and reports

Per audience request

• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

Analysis of microbial communities for biotransformation, biodegradation and...

Tue, 25 Mar 2025 11:01:07 GMT

Geomicrobiology and petroleum microbiology are important fields that study how microbes interact with geological, geochemical, and petroleum processes. Understanding the composition of microbial communities can advance our knowledge of biotransformation, biodegradation, and bioremediation in industries such as environmental engineering, mining, and oil and gas.

QIAGEN CLC Genomics Workbench and the Microbial Genomics Module provide tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, and functional metagenomics. This webinar will focus on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering) using data collected from oil reservoirs. Specifically, the trainer will be:

• Highlighting different tools within the MGM application and research areas supported

• For taxonomic profiling:

o Importing data

o Utilizing metadata

o Downloading and managing references

o Launching the OTU clustering workflow (analytical pipeline)

• Downstream processing of abundance tables

• Creating and exporting high-quality graphics

Long reads analysis with QIAGEN CLC Genomics Workbench

Tue, 25 Feb 2025 20:59:02 GMT

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Thu, 13 Feb 2025 16:06:53 GMT

In this training, the trainer will go over

• The basics of workflow construction

• How to visualize different steps of the workflow and customize different settings

• How to edit workflows (add/remove steps, lock/unlock parameters and more)

• How to share workflows

• How to install workflows

• Other workflow related topics

What's new in QIAGEN CLC Genomics version 25

Sun, 26 Jan 2025 23:17:36 GMT

Single - cell RNA-seq, cell hashing and spatial transcriptomics

Thu, 23 Jan 2025 13:42:27 GMT

In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:

• Import your raw FASTQ or processed cell-matrix files.

• Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.

• Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.

o Dimension reduction (UMAP, t-SNE) plots

o Differential expression table for clusters, cell types, or combination of both

o Heat map

o Dot plots

o Violin plots

• Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).

• Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

Sanger sequencing, alignment, cloning, primer design and more using QIAGEN...

Thu, 23 Jan 2025 12:52:40 GMT

This training will be relevant to both QIAGEN Main and Genomics workbench users and prospects who are interested in below analytics.

• Alignment and tree construction

• Sanger sequencing analysis

• Cloning and primer design

• Other molecular biology tools

Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) with...

Mon, 22 Jul 2024 15:37:11 GMT

You asked, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).

In this training, we’ll cover:
• Introduction to AMR, MLST and relevant databases
• QIAGEN Microbial Insight - Antimicrobial Resistance database (QMI-AR)
• Importing data and downloading needed databases
• Finding resistance with nucleotide DB, PointFinder and ShortBRED
• Integrating AMR with MLST
• Exporting high-resolution graphics and result tables.

De novo assembly, BLAST and genome finishing with QIAGEN CLC Genomics Workbench

Thu, 18 Jul 2024 18:31:45 GMT

Participants will learn the following:
o Download and install needed plugins.
o Import data required for the analysis.
o Run the de novo assembly workflow.
o For long reads, improve a de novo assembly by polishing with short, high-quality reads.
o Map reads to a reference and visualize an assembly.
o For long reads, correct raw long reads for further analysis.
o Use BLAST to investigate the contigs.
o Analyze and assemble contigs through Genome Finishing tools.

Streamline H5N1 and other microbial samples with CLC Genomics Workbench

Thu, 23 May 2024 15:17:00 GMT

In this training, you will learn how to analyze viral samples using QIAGEN CLC Genomics Workbench. This webinar will focus on bioinformatics workflows and data interpretation using H5N1 as an example, but similar analysis can be done with other viral and microbial (bacteria, fungus and more) samples.

Using viral samples, you will learn how to:

• Utilize molecular biology tools such as primer design, cloning, alignment and tree construction and Sanger sequencing analysis
• Profile the virus present in a sample and automatically generate read mappings, detect variants, annotate consensus sequences, BLAST annotated consensus sequence genes and build phylogenetic trees for top hits and their close relatives
• Microbial genomics analysis including OTU clustering, taxonomic profiling and functional analysis
• Additional topics of interest based on registration feedback

QIAGEN CLC Genomics Workbench is a user-friendly bioinformatics software solutions for genomics, transcriptomics, epigenomics and metagenomics analysis in one program.

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Thu, 22 Feb 2024 08:40:00 GMT

In this training, the trainer will go over
• The basics of workflow construction
• How to visualize different steps of the workflow and customize different settings
• How to edit workflows (add/remove steps, lock/unlock parameters and more)
• How to share workflows
• How to install workflows
• Other workflow related topics

Long reads analysis using QIAGEN CLC Genomics workbench (with new features -...

Tue, 13 Feb 2024 13:25:00 GMT

This webinar will introduce users to the long read support plugin for Oxford Nanopore and PacBio sequencing reads in QIAGEN CLC Genomics Workbench.

Participants will learn the following:

• Download and install needed plugins.
• Import data required for the analysis.
• Long read de novo assembly.
• Map reads to a reference and visualize an assembly.
• Use BLAST to investigate the contigs.
• Additional long read tools: polish with short reads, structural variant calling.
• Genome finishing tools: analyze and assemble contigs
• Analytical tools: RNA-seq analysis for long reads, classify long read amplicons for metagenomics.

What’s new in QIAGEN CLC Genomics Workbench version 24

Wed, 31 Jan 2024 14:19:21 GMT

QIAGEN CLC Genomics Workbench version 24 is here with exciting updates we'd like to share with you. These include:

Our QIAGEN CLC LightSpeed Module which now provides ultrafast somatic workflows
Spatial Transcriptomics and ParseBio support in QIAGEN CLC Single Cell Analysis Module
Amplicon classification for ONT reads in QIAGEN CLC Microbial Genomics Module
New Structural variant detection for long read and De novo assembly of PacBio HiFi reads
Importer for Element, PacBio Onso, Ultima reads, Singular
CRAM format importer / exporter
Fancy new interactive RNAseq Volcano plot for RNAseq
And many more new and improved workflow and reporting capabilities
Join this webinar to:

Learn how to take advantage of the latest improvements
Get an overview of the many tools available to you
Make sure to join this webinar to elevate your understanding of current trends in bioinformatics

Circulating Tumor Cell Detection and Analysis to Support Malignancy...

Wed, 25 Oct 2023 14:11:11 GMT

Circulating tumor cells (CTCs) are cells that leave the primary tumor and are intravasated into the blood circulation system. A subset of those make it to other organs and are responsible for metastasis. iCellate’s CellMate platform is a CTC-based liquid biopsy for cancer cell enrichment, detection, and biomarker analysis via a simple blood draw.

In this seminar, you’ll learn:

From Helena Silva Cascales, senior scientist at iCellate Medical AB, how the isolation of whole-tumor cells provides a more comprehensive biomarker analysis, including genomic sequencing and multiplexed protein expression analysis.
From Kashyap Dave, principal scientist at iCellate Medical AB, how DNA from single CTCs can be amplified, sequenced, and analyzed to support malignancy designation and tissue of origin identification using classification analyses under development within Qiagen CLC Genomics Workbench.

Part I: Single-cell RNA sequencing data analysis using QIAGEN CLC Genomics...

Mon, 21 Aug 2023 20:06:25 GMT

This two-part series will walk you through single-cell RNA sequencing (scRNA-seq) analysis starting with a matrix file or FASTQ files and ending with a deep understanding of key pathways, regulators and cell type signatures within your data.

This session is for part I of this training. In this session, you'll learn to use QIAGEN CLC Genomics Workbench to perform secondary analysis on your scRNA-seq data. Specifically, you will learn how to:
• Import your raw FASTQ or processed cell-matrix files
• Use pre-configured but customizable pipelines/workflows for scRNA-seq data
• Generate high-resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries. These include:

o UMAP, t-SNE plots
o Differential expression table for clusters, cell types, or a combination of both
o Heat map
o Dot plots
o Violin plots

Part II of this training takes place on Wednesday, Aug. 16. It focuses on interpreting scRNA-seq data using QIAGEN Ingenuity Pathway Analysis (IPA) to understand key pathways, regulators and cell type signatures within your data. Click here to watch Part II: https://tv.qiagenbioinformatics.com/video/87882212/part-ii-single-cell-rna-sequencing

Immune repertoire analysis using QIAGEN CLC Genomics Workbench

Mon, 21 Aug 2023 15:57:03 GMT

The composition of the immune repertoire, consisting of the T cell and B cell receptors (TCR and BCR), is important for an organism's adaptive immune system and plays a pivotal role in an individual's overall health. Understanding the complex array of TCR and BCR allows for developing precision medicine and immunotherapy. Analyzing next-generation sequencing (NGS) data from RNA-seq experiments to characterize and understand TCR and BCR clonotypes may aid in identifying cases that could benefit from personalized immunotherapy or potentially predict therapeutic outcomes.

In this training, we'll use QIAGEN CLC Genomics Workbench to analyze immune repertoire NGS data generated from RNA-seq or single-cell RNA-seq data. Together we'll explore how to import, analyze and interpret your NGS data. Specifically, you'll learn how to:

-Import NGS data into QIAGEN CLC Genomics Workbench

-Analyze the data using template workflows

-Interpret the results using the interactive graphics produced by the workflows

Pathogen detection in wastewater samples using QIAGEN CLC Genomics Workbench

Mon, 24 Apr 2023 18:22:10 GMT

In this 90-minute training, you will learn how to easily analyze wastewater samples to detect pathogens (SARS-COV2, etc.) using QIAGEN CLC Genomics Workbench software.

You will learn how to:
• Importing reads
• Open and modify prebuilt workflow (analysis pipeline)
• Install and execute workflow
• Review QC reports
• Perform genome visualization
• Export the consensus sequence in FASTA format to upload to Pangolin
• Create a SNP tree of the consensus sequence and overlay Pangolin information
• Export graphical and tabular results

What’s new in QIAGEN CLC Genomics Workbench version 23

Fri, 03 Feb 2023 04:39:22 GMT

QIAGEN CLC Genomics Workbench version 23 is here with exciting updates we'd like to share with you. These include:

Our new QIAGEN CLC LightSpeed Module which provides the world’s fastest and cheapest whole genome sequencing (WGS) and (WES) analyses
Our new and improved QIAGEN CLC Cloud Module which provides direct access to your AWS S3 files and frees up your local workbench resources
New capabilities in QIAGEN CLC Microbial Genomics Module
New analyses in QIAGEN CLC Single Cell Analysis Module
New cloning tools
And many more new and improved workflow capabilities

16S/18S/ITS sequencing analysis using CLC Genomics Workbench

Wed, 25 Jan 2023 17:30:08 GMT

QIAGEN CLC Microbial Genomics Module provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training will be focused on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering). The trainer will cover:

· Overview of different tools within QIAGEN CLC Microbial Genomics Module and research areas supported

· For taxonomic profiling

o Importing data

o Utilization of metadata

o Downloading and managing references

o Walk through of OTU clustering workflow (analytical pipeline)

o Downstream processing of abundance tables

o Creating and exporting high-quality graphics

Extracting novel hypotheses and insights from single cell data

Fri, 20 May 2022 15:37:45 GMT

Follow us on a journey of single cell data exploration. See how you can Process, Analyze, Compare, and Contextualize, your results to identify novel biological relationships and drive new hypotheses. In this presentation, Dr. Jean-Noel Billaud, PhD, will take you from data to biological insight using human single cell fetal liver data.

Participants will learn:
• Process: Which tools and workflows are best suited to process scRNA-seq data
• Analyze: How to analyze, highlight and identify cell types of interest
• Compare: How you can effortlessly compare and discover similar biology phenomena
• Contextualize: Provide context from other tissues and diseases to unlock hidden biology

Speaker:

Jean-Noel Billaud, PhD

Dr. Jean-Noel Billaud. Jean-Noël is a Senior Principal Scientist at QIAGEN Digital Insights. Before joining QIAGEN, he was part of Ingenuity Systems since 2008 as a staff scientist. Dr, Billaud holds a Ph.D. in Blood Cell Biology from Paris and did his post-doctoral work at the Scripps Research Institute (San Diego, CA). He previously worked at the Vaccine Research Institute of San Diego and co-developed a universal vaccine platform to target infectious disease, metabolic diseases, and cancer.