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Tutorials

Basic Tutorials

  • Screen Shot 2013-05-06 at 14.55.30 PM

    An Introduction to Workflows

    Biomedical Genomics Workbench, CLC Genomics Workbench

    Create, edit and manage workflows in your workbench.

    Available both as a pdf tutorial and a video tutorial.

  • Assemble Sequences to a Reference

    CLC Genomics Workbench, CLC Main Workbench

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

  • BLAST Searches

    CLC Genomics Workbench, CLC Main Workbench

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

  • Folding RNA Molecules

    CLC Genomics Workbench, CLC Main Workbench

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

  • Gateway Cloning

    CLC Genomics Workbench, CLC Main Workbench

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

  • getting-started

    Getting Started

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

    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 both as a pdf tutorial and a video tutorial.

  • Molecular Biology Basics

    CLC Genomics Workbench, CLC Main Workbench

    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.

  • Phylogenic Trees and Metadata

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

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

High-Throughput Analysis

  • ChIP Sequencing

    CLC Genomics Workbench

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

  • Comparative Analysis of Three Bovine Genomes

    CLC Genomics Workbench

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

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    De Novo Assembly and BLAST

    CLC Genomics Workbench

    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 both as a pdf tutorial and a video tutorial.

  • De Novo Assembly of Paired Data

    CLC Genomics Workbench

    An introduction to how to import fastaq paired data, run a sequence quality report, trim the data, and run a De Novo assembly with scaffolding.

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    Expression Analysis with the Advanced RNA-Seq Plugin

    CLC Genomics Workbench

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

    Available both as a pdf tutorial and a video tutorial.

  • Microarray-Based Expression Analysis

    CLC Genomics Workbench, CLC Main Workbench

    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.

  • Read Mapping in Detail

    CLC Genomics Workbench

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

  • Reference Genome and Annotations Tracks

    CLC Genomics Workbench

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

  • Resequencing Analysis using Tracks

    CLC Genomics Workbench

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

  • Resequencing – Map Reads to Reference and Variant Detection

    CLC Genomics Workbench

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

  • Small RNA Analysis

    Biomedical Genomics Workbench, CLC Genomics Workbench

    How to go 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.

  • Visualize Variants on Protein Structure

    Biomedical Genomics Workbench, CLC Genomics Workbench

    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.

Drug Discovery

  • Dock Ligands from a 2D Sketch

    CLC Drug Discovery Workbench

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

  • Exploring Protein-Ligand Binding

    CLC Drug Discovery Workbench

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

  • Exploring your Protein

    CLC Drug Discovery Workbench

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

  • Find and Align Binding Pockets

    CLC Drug Discovery Workbench

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

  • Getting Started (Drug)

    CLC 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.

  • Virtual Screening

    CLC Drug Discovery Workbench

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

Additional Tutorials

  • Bisulfite-Sequencing

    Biomedical Genomics Workbench, CLC Genomics Workbench

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

  • Genome Finishing Module – Using the Align Contigs Tool

    CLC Genomics Workbench

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

  • microbiome

    Microbiome Profiling Using workflows

    Biomedical Genomics Workbench, CLC Genomics Workbench

    User will 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 both as a pdf tutorial and a video tutorial.

  • OTU Clustering and Analysis of Microbial Communities

    Biomedical Genomics Workbench, CLC Genomics Workbench

    This tutorial will take you through the different tools available in the 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.

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    Typing and Epidemiological Clustering of Common Pathogens (beta)

    Biomedical Genomics Workbench, CLC Genomics Workbench

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

    Available both as a pdf tutorial and a video tutorial.

  • Whole Metagenome Functional Analysis (beta)

    Biomedical Genomics Workbench, CLC Genomics Workbench

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

Cancer Research

  • Batching of Multi-Input Workflows

    Biomedical Genomics Workbench

    This tutorial will demonstrate how workflows that have more than one input can be run in batch mode. This is the case of 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 fours, as well as workflows that compare tumor to normal samples.

  • ChIP Sequencing Using Biomedical Genomics Workbench

    Biomedical Genomics Workbench

    This tutorial takes you through a complete ChIP sequencing workflow using Biomedical Genomics Workbench.

  • Copy Number Variant Detection

    Biomedical Genomics Workbench

    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 CNVs regions where the normalized coverage of the sample to be analyzed differs from the control samples in a statistically significant way.

  • Expression Analysis with the Advanced RNA-Seq and Ingenuity Pathway Analysis Solution

    Biomedical Genomics Workbench

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

  • Find Very Low Frequency Variants With QIAGEN GeneRead Panels

    Biomedical Genomics Workbench

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

  • finding

    Finding a Rare Disease Causing Variant

    Biomedical Genomics Workbench

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

    Available both as a pdf tutorial and a video tutorial.

  • Identification of Somatic Variants in a Matched Tumor-Normal Pair

    Biomedical Genomics Workbench

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

  • Identification of Variants in a Tumor Sample

    Biomedical Genomics Workbench

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

  • Identification of Variants Using GATK

    Biomedical Genomics Workbench

    This tutorial demonstrates the usability of the GATK Integration Plugin with a small dataset, and shows how the variants identified using GATK can be annotated and visualized with the tools included in Biomedical Genomics Workbench.

  • Modification of an Existing Workflow

    Biomedical Genomics Workbench

    In this tutorial we will try to 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.

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    RNA-Seq Analysis of Human Breast Cancer Data

    Biomedical Genomics Workbench

    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 both as a pdf tutorial and a video tutorial.