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Tutorials

Basic Tutorials

  • An Introduction to Annotation Tracks

    CLC Genomics Workbench

    How to add valuable information to an existing reference track in the CLC Genomics Workbench.

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    Getting Started

    CLC Cancer Research Workbench, CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    A guide to the most basic steps of working with CLC Genomics Workbench, CLC Cancer Research Workbench, CLC Main Workbench, and CLC Sequence Viewer.

    Available both as a pdf tutorial and a video tutorial.

  • Side Panel Settings

    CLC Cancer Research Workbench, CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    How to use the Side Panel to change the way your sequences, alignments and other data are shown.

  • View a DNA Sequence

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    This brief tutorial takes you through some different ways to display a sequence in CLC Main Workbench and CLC Genomics Workbench.

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.

  • ChIP Sequencing: The Basics (Legacy)

    CLC Genomics Workbench

    A demonstration of a ChIP sequencing workflow using CLC Genomics Workbench 5.0 to 7.0.

  • ChIP Sequencing: Understanding the Details (Legacy)

    CLC Genomics Workbench

    This tutorial takes you through some of the details of the ChIP-seq analysis in the CLC Genomics Workbench 5.0 to 7.0.

  • Comparative analysis of three bovine genomes

    CLC Genomics Workbench

    This tutorial takes you through some of the tools for identifying species-specific variants. We identify exome variations that are unique for one of three different species and attempt to link the variations to altered pathways with the gene ontology tool that is built into CLC Genomics Workbench.

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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.

  • Expression Analysis – Part I

    CLC Genomics Workbench, CLC Main Workbench

    This tutorial is intended to show a straight-forward example of how to identify and interpret the differentially expressed genes in samples from two different tissues.

  • Expression Analysis – Part II

    CLC Genomics Workbench, CLC Main Workbench

    Examining various methods to perform quality control of the data used in Part 1.

  • Expression Analysis – Part III

    CLC Genomics Workbench, CLC Main Workbench

    Identifying and investigating the genes that are differentially expressed.

  • Expression Analysis – Part IV

    CLC Genomics Workbench, CLC Main Workbench

    Annotating the gene list and using the annotations to see if there is a pattern in the biological annotations of the genes in the list of candidate differentially expressed genes.

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    Introduction to Workflows

    CLC Cancer Research Workbench, CLC Genomics Workbench

    This tutorial introduces the Workflow tool through creating a workflow containing analyses steps from CLC Genomics Workbench and CLC Cancer Research Workbench.

    Available both as a pdf tutorial and a video tutorial.

  • Read Mapping in Detail

    CLC Genomics Workbench

    This tutorial is about running read mappings.

  • Reference Genome Tracks

    CLC Genomics Workbench

    This tutorial introduces two ways to create reference genome tracks in the CLC Genomics Workbench.

  • Resequencing Analysis using Tracks

    CLC Genomics Workbench

    A basic analysis of two samples is used to demonstrate some of the functionality available in the CLC Genomics Workbench for targeted resequencing projects, including working with track-based data.

  • Resequencing – Map Reads to Reference and Variant Detection

    CLC Genomics Workbench

    This tutorial goes through the basics of running a read mapping followed by a variant detection analysis.

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    RNA-Seq Analysis – Part I (Legacy)

    CLC Genomics Workbench

    Covering the basics steps of running an RNA-seq Analysis with an annotated reference genome.

    Available both as a pdf tutorial and a video tutorial.

  • RNA-Seq Analysis – Part I (Tracks)

    CLC Genomics Workbench

    Covering the basics steps of running an RNA-seq analysis in track format with an annotated reference genome.

  • RNA-Seq Analysis – Part II (Legacy)

    CLC Genomics Workbench

    This tutorial covers RNA-seq analysis with focus on non-specific matches and expression measures.

  • RNA-Seq Analysis – Part II (Tracks)

    CLC Genomics Workbench

    This tutorial covers RNA-seq analysis on tracks with focus on non-specific matches and expression measures.

  • RNA-Seq Analysis – Part III (Legacy)

    CLC Genomics Workbench

    In this tutorial we will focus on discovery of new putative exons.

  • RNA-Seq Analysis – Part III (Tracks)

    CLC Genomics Workbench

    In this tutorial we will focus on the statistical analysis of differentially expressed genes and transcripts from your RNA-seq samples.

  • RNA-Seq Analysis – Part IV (Legacy)

    CLC Genomics Workbench

    This tutorial is focusing on quality control in RNA-Seq analysis

  • Visualize variants on protein structure

    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

  • Aligning Sequences

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    Outlining some of the alignment functionalities of CLC Main Workbench.

  • Assembly

    CLC Genomics Workbench, CLC Main Workbench

    In this tutorial, you will see how to assemble data from automated sequencers into a contig and how to find and inspect any conflicts that may exist between different reads.

  • BLAST

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    This tutorial takes you through the steps of running a blast search in CLC Workbenches

  • Detect Restriction Site

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    How to find restriction sites and annotate them on a sequence.

  • 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

    How to use the Workbench tool for in silica Gateway Cloning.

  • Getting started: Analysis of Microbial Communities

    Biomedical Genomics Workbench, CLC Genomics Workbench

    Mr. X is a suspect in a murder. The body was found on site 1, but Mr. X claims he was never there because he spent his entire week-end on site 2 and 3. Investigators have found a pair of rubber boots and a pair of hiking shoes at Mr. X's house. Both were dirty with soil on the soles. They took 3 samples of soil from each pair of shoes, and 2 samples of soil from each site: the crime scene (site 1) but also the 2 sites Mr. X claimed he was at (site 2 and 3).

  • In Silico Cloning Workflow

    CLC Genomics Workbench, CLC Main Workbench

    Learn how to make a virtual PCR-amplification of a gene using primers with restriction sites at the 5′ ends and how to insert the gene into a multiple cloning site of an expression vector.

  • Microbial Genome Finishing Module – Using the Align Contigs Tool

    CLC Genomics Workbench

    How to use the Align Contigs tool to identify and join overlapping contigs, and split misassembled contigs.

  • 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 to estimate alpha and beta diversities in microbial samples.

  • Phylogeny Module - Visualization of Trees and Meta Data

    CLC Genomics Workbench, CLC Main Workbench, CLC Sequence Viewer

    This tutorial will briefly introduce reconstruction of phylogenetic trees and visualization of these with the new tree viewer. The main focus in this tutorial is the visualization of metadata as a powerful tool for analyzing your data.

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    Primer Design

    CLC Genomics Workbench, CLC Main Workbench

    Find out how to use the CLC Main Workbench and CLC Genomics Workbench to find primers for PCR amplification of a specific region.

    Available both as a pdf tutorial and a video tutorial.

  • Tips for Specialized BLAST Searches.

    CLC Genomics Workbench, CLC Main Workbench

    BLAST tips: Find out how to locate a protein sequence on the chromosome.

  • Working with Annotations

    CLC Genomics Workbench, CLC Main Workbench

    This tutorial highlights the areas of the Workbench where you can work with annotations.

Cancer Research

  • 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.

  • 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.

  • 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.

  • 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.

  • Visualize variants on protein structure

    Biomedical 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.