Tutorials

Introduction


An introduction to workflows

Create, edit, and manage workflows in your workbench. http://tv.qiagenbioinformatics.com/video/11806268/introduction-to-workflows

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Assemble sequences to a reference

Assemble Sanger sequences into contigs to find - and resolve - conflicts between reads.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench

BLAST searches

Learn about the different BLAST searches and options available in the workbench.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench

Visualize variants on protein structure

This tutorial will show you how to link variants to positions on a 3D protein structure, and how to interpret the resulting interactive 3D model. The focus will be on identifying variants associated with drug resistance to chronic myeloid leukemia treatment.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Phylogenic trees and metadata

Learn how to reconstruct a phylogeny and visualize metadata on the tree.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

Molecular biology basics

Use the tools and functionalities of the workbench to simplify your cloning strategy and visualize every steps of the process: Look for restriction enzymes, design primers, and simulate your cloning strategy and results.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench

Getting started

A guide to the most fundamental functionalities of your workbench: Learn how to import data in the workbench, how to run a tool and use the toolbar and side panels settings to visualize your results in different ways.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

Gateway cloning

Facilitate your Gateway cloning work with the Vector NTI Import plugin.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench

Required plugin: Vector NTI Import (non-commercial)

Folding RNA molecules

Learn how to predict the secondary structure of an RNA molecule.

Available as a PDF tutorial

CLC Genomics Workbench, CLC Main Workbench

Next generation sequencing


Bisulfite sequencing

Find methylated cytosines and identify regions with high methylation levels in your sequencing reads using the Bisulfite sequencing plugin.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Required plugin: Bisulfite Sequencing (non-commercial)

ChIP sequencing

This tutorial takes you through a complete ChIP sequencing workflow using CLC Genomics Workbench. The tutorial makes use of the peak-shape based ChIP-seq Analysis tool present in CLC Genomics Workbench 7.5.

Available as a PDF tutorial

CLC Genomics Workbench

Resequencing analysis using tracks

Find and annotate cancer specific variants by comparing normal and cancer tissue reads and by filtering for variants leading to amino acid changes.

Available as a PDF tutorial

CLC Genomics Workbench

Resequencing – map reads to reference and variant detection

Go through the steps of a typical resequencing analysis - mapping reads to a reference and finding variants - using E. coli reads from a 454 sequencer.

Available as a PDF tutorial

CLC Genomics Workbench

Reference genome and annotation tracks

Learn how to create a reference genome and manage track lists to visualize your data and associated annotations.

Available as a PDF tutorial

CLC Genomics Workbench

Read mapping in detail

Understand the parameters of the Map Reads to Reference tool, and the impact of using paired end data on the mapping results.

Available as a PDF tutorial

CLC Genomics Workbench

Comparative analysis of three bovine genomes

Learn how to identify species-specific variants, filter those leading to amino acid changes, and associate relevant species-specific pathways.

Available as a PDF tutorial

CLC Genomics Workbench

CLC Genome Finishing Module - using the Align Contigs tool

Learn how to manually join or split contigs using the Align Contigs tool of Genome Finishing Module.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Required plugin: CLC Genomics Finishing Module (commercial)

De novo assembly and BLAST

This tutorial highlights some of the tools for a typical de novo sequencing workflow with a data set from a high-throughput sequencing machine.

Available as a PDF tutorial

CLC Genomics Workbench

De novo assembly of paired data

An introduction to how to import fastq paired data, run a sequence quality report, trim the data, and run a de novo assembly with scaffolding.

Available as a PDF tutorial

CLC Genomics Workbench

Expression analysis


Small RNA analysis

This tutorial goes through the initial parts of analyzing a small RNA data set: Trim off adapter sequences, extract, count, and annotate small RNAs to identify known miRNAs and other non-coding RNAs.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

RNA-seq analysis of human breast cancer data

This tutorial gives a brief overview of how to analyze RNA-seq data using Biomedical Genomics Workbench. To reduce the processing time required by the workbench to run the RNA-seq analysis and thereby be able to complete the tutorial, we will work with a subset of publicly available RNA-seq data.

Available as a PDF tutorial

Biomedical Genomics Workbench

Required plugin: Ingenuity Pathway Analysis plugin (non-commercial). An active IPA account is required.

Microarray-based expression analysis

Perform data quality control, identify differentially expressed genes, and interpret your results in a biological context using annotations. This tutorial is based on microarray data but many tools are applicable to RNA-seq.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench, CLC Main Workbench

Expression analysis using RNA-Seq data

Discover the powerful statistical analysis tools from the Advanced RNA-Seq plugin.

Available as a PDF tutorial

CLC Genomics Workbench

Required plugin: Advanced RNA-Seq (non-commercial)

RNA-Seq with Ingenuity Pathway Analysis

This tutorial demonstrates the collaborative power of RNA-Seq Analysis and Ingenuity Pathway Analysis plugin to analyze and interpret RNA-seq expression data.

Available as a PDF tutorial

Biomedical Genomics Workbench

Required plugins: Advanced RNA-Seq (non-commercial), Ingenuity Pathway Analysis plugin (non-commercial). Use of the IPA plugin requires an active IPA account.

Biomedical research


Finding a rare disease causing variant

Learn how to take advantage of the Ingenuity Variant Analysis plugin for Biomedical Genomics Workbench to find a list of variants specific to a proband's genome and filter them for interpretation.

Available as a PDF tutorial

Biomedical Genomics Workbench

Required plugin: Ingenuity Variant Analysis plugin (non-commercial). The plugin requires an active IPA account.

Batching of multi-input workflows

This tutorial will demonstrate how workflows that have more than one input can be run in batch mode. This is the case for most of the ready-to-use workflows available in the toolbox of Biomedical Genomics Workbench, e.g. all workflows that analyze a trio or a family of four, as well as workflows that compare tumor to normal samples.

Available as a PDF tutorial

Biomedical Genomics Workbench

Identification of variants in a tumor sample

This tutorial will guide you through the process of identifying variants and verifying them.

Available as a PDF tutorial

Biomedical Genomics Workbench

Identification of somatic variants in a matched tumor-normal pair

This tutorial will guide you through the process of identifying somatic variants from a matched tumor/normal sample pair from one patient.

Available as a PDF tutorial

Biomedical Genomics Workbench

Find very low frequency variants with QIAGEN GeneRead Panels

This tutorial uses the capacities of Biomedical Genomics Workbench and the QIAGEN GeneRead Panels plugin to find very low frequency variants in targeted amplicon sequences generated using a QIAGEN GeneRead DNAseq Targeted Panels V2 kit.

Available as a PDF tutorial

Biomedical Genomics Workbench

Copy number variant detection

Copy number variants are amplifications and deletions of exon and chromosome fragments as well as whole exons or chromosomes. The copy number variant detection algorithm is designed to detect copy number variations (CNVs) from targeted resequencing experiments. These can be either gene panels or whole exome sequencing. It identifies CNV regions where the normalized coverage of the sample to be analyzed differs from the control samples in a statistically significant way.

Available as a PDF tutorial

Biomedical Genomics Workbench

Find actionable variants with QIAseq Panels

This tutorial uses the capacities of the Biomedical Genomics Workbench and the QIAseq DNA V3 Panel Analysis Plugin to find actionable variants - even at very low frequencies - in Targeted Amplicons sequences generated using a BRCA1 and BRCA2 QIAseq panel kit.

Available as a PDF tutorial

Biomedical Genomics Workbench

Modification of an Existing Workflow

Ready-to-use workflows are provided in Biomedical Genomics Workbench for different applications and scenarios. However, there may be situations where you would like to extend an analysis or customize it to special needs. In this tutorial we modify the Identify Somatic Variants from Tumor Normal Pair (WES) ready-to-use workflow to include the step in which we remove variants present in HapMap.

Available as a PDF tutorial

Biomedical Genomics Workbench

Microbial genomics


Whole metagenome functional analysis (beta)

Assemble metagenomes derived from two different groups of samples and investigate their functional differences.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Required plugins: CLC Microbial Genomics Module (commercial), MetaGeneMark (commercial)

Typing and epidemiological clustering of common pathogens (beta)

This tutorial will take you through the tools available in CLC Microbial Genomics Module to perform typing and epidemiological study of cultured bacteria using the metadata functionalities of the Microbial Genomics module.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Required plugin: CLC Microbial Genomics Module (commercial)

OTU clustering step by step

This tutorial will take you through the different tools available in CLC Microbial Genomics Module and CLC Genomics Workbench to perform OTU clustering and estimate alpha and beta diversities of microbial communities with the Microbial Genomics module.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Plugin required: CLC Microbial Genomics Module (commercial)

OTU clustering using workflows

Learn how to identify individual constituents of a microbial community, and how to identify microbiome profiles that can be associated with certain sample parameters (metadata). In this example we solve a forensics case where the microbiome of the soil on a suspects boots can be associated with the soil microbiome at a crime scene.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Required plugin: CLC Microbial Genomics Module (commercial)

Taxonomic profiling of whole shotgun metagenomic data

Learn how easy it is to monitor the evolution of a microbiota over time using the taxonomic profiling tools from CLC Microbial Genomics Module.

Available as a PDF tutorial

Biomedical Genomics Workbench, CLC Genomics Workbench

Drug discovery


Virtual screening

How to set up and run a virtual screening and inspect the results.

Available as a PDF tutorial

CLC Drug Discovery Workbench

Getting Started (Drug Discovery Workbench)

The user interface is introduced, and it is explained how to import your own existing data. Furthermore, 10 tips to get the most out of the workbench are presented.

Available as a PDF tutorial

CLC Drug Discovery Workbench

Find and align binding pockets

The Find Binding Pockets and Align Protein Structure tools are used to further explore your target protein.

Available as a PDF tutorial

CLC Drug Discovery Workbench

Exploring your protein

Taking you through some of the sequence analysis and structure visualization features you can use to get to know your target protein.

Available as a PDF tutorial

CLC Drug Discovery Workbench

Exploring protein-ligand binding

Protein-ligand binding is explored using molecular docking, to fit the ligand in a binding pocket on the target protein.

Available as a PDF tutorial

CLC Drug Discovery Workbench

Dock ligands from a 2D sketch

Fast track docking with copy-paste of molecule from 2D sketcher software and one-click docking. This tutorial describes how to download and use the freely available program Balloon, which is needed to support the copy-paste of 2D molecule sketches.

Available as a PDF tutorial

CLC Drug Discovery Workbench

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