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Introduction to CLC Genomics Workbench
- Contact information and citation
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- Plugins
- Network configuration
- CLC Server connection
- Getting started and latest improvements
User interface
- View Area
- Zoom and selection in View Area
- Toolbox and Favorites tabs
  - Toolbox tab
  - Favorites tab
- Processes tab and Status bar
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Working with tables
  - Filtering tables
- Customized attributes on data locations
- Local search
  - Quick search
  - Advanced search
User preferences and settings
- General preferences
- View preferences
  - Import and export Side Panel settings
- Data preferences
- Advanced preferences
- Export/import of preferences
- View settings for the Side Panel
Printing
- Selecting which part of the view to print
- Page setup
- Print preview
Import/export of data and graphics
- Standard import
  - External files
- Import tracks
  - GFF3 format
  - VCF import
- Import high-throughput sequencing data
- Import RNA spike-in controls
- Import Primers
  - Import Primer Pairs
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- CLC Server data import and export
- Copy/paste view output
Data download
- Search for Sequences at NCBI
  - NCBI search options
  - Handling of NCBI search results
- Search for PDB Structures at NCBI
- Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
- SRA search
- Sequence web info
References management
- Download Genomes
- QIAGEN Sets
- Custom Sets
- Imported Data
  - Exporting reference data outside of the Reference Data Manager framework
Running tools, handling results and batching
- Running tools
  - Running a tool on a CLC Server
- Handling results
- Batch processing
Metadata
- Creating metadata tables
  - Importing metadata
  - Creating a metadata table directly in the Workbench
- Associating data elements with metadata
  - Associate Data Automatically
  - Associate Data with Row
- Working with data and metadata
- Moving, copying and exporting metadata
- Editing Metadata tables
Workflows
- Creating a workflow
- Editing existing workflows
  - Snippets in workflows
  - Workflow visualization
- Workflow elements
- Launching workflows individually and in batches
- Batching part of a workflow
- Advanced workflow batching
- Managing workflows
Viewing and editing sequences
- View sequence
- Circular DNA
  - Using split views to see details of the circular molecule
  - Mark molecule as circular and specify starting point
- Working with annotations
- Element information
- View as text
- Sequence Lists
BLAST search
- Running BLAST searches
  - BLAST at NCBI
  - BLAST against local data
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
- Bioinformatics explained: BLAST
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking sequence and structure
- Align Protein Structure
  - Example: alignment of calmodulin
  - The Align Protein Structure algorithm
- Generate Biomolecule
General sequence analyses
- Extract sequences
- Shuffle sequence
- Dot plots
- Local complexity plot
- Sequence statistics
  - Bioinformatics explained: Protein statistics
- Join Sequences
- Pattern discovery
  - Pattern discovery search parameters
  - Pattern search output
- Motif Search
- Create motif list
Nucleotide analyses
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse complements of sequences
- Translation of DNA or RNA to protein
- Find open reading frames
  - Open reading frame parameters
Protein analyses
- Protein charge
- Antigenicity
- Hydrophobicity
  - Hydrophobicity graphs along sequence
  - Bioinformatics explained: Protein hydrophobicity
- Download Pfam Database
- Pfam domain search
- Find and Model Structure
  - Create structure model
  - Model structure
- Secondary structure prediction
- Protein report
- Reverse translation from protein into DNA
  - Bioinformatics explained: Reverse translation
- Proteolytic cleavage detection
  - Bioinformatics explained: Proteolytic cleavage
Primers
- Primer design - an introduction
  - General concept
  - Scoring primers
- Setting parameters for primers and probes
  - Primer Parameters
- Graphical display of primer information
  - Compact information mode
  - Detailed information mode
- Output from primer design
- Standard PCR
- Nested PCR
- TaqMan
- Sequencing primers
- Alignment-based primer and probe design
- Analyze primer properties
- Find binding sites and create fragments
  - Binding parameters
  - Results - binding sites and fragments
- Order primers
Sequencing data analyses
- Importing and viewing trace data
  - Trace settings in the Side Panel
- Trim sequences
  - Trimming using the Trim tool
  - Manual trimming
- Assemble sequences
- Assemble sequences to reference
- Sort sequences by name
- Add sequences to an existing contig
- View and edit contigs and read mappings
- Reassemble contig
- Secondary peak calling
- Extract Consensus Sequence
- Combine Reports
  - Combine Reports output
Cutting and cloning
- Restriction site analyses
  - Dynamic restriction sites
  - Restriction Site Analysis
- Restriction enzyme lists
- Molecular cloning
- Gateway cloning
- Gel electrophoresis
  - Gel view
Sequence alignment
- Create an alignment
- View alignments
  - Bioinformatics explained: Sequence logo
- Edit alignments
  - Realignment
- Join alignments
- Pairwise comparison
  - The pairwise comparison table
  - Bioinformatics explained: Multiple alignments
Phylogenetic trees
- K-mer Based Tree Construction
- Create tree
- Model Testing
- Maximum Likelihood Phylogeny
  - Bioinformatics explained
- Tree Settings
- Metadata and phylogenetic trees
RNA structure
- RNA secondary structure prediction
- View and edit secondary structures
- Evaluate structure hypothesis
  - Selecting sequences for evaluation
  - Probabilities
- Structure scanning plot
  - Selecting sequences for scanning
  - The structure scanning result
- Bioinformatics explained: RNA structure prediction by minimum free energy minimization
  - The algorithm
  - Structure elements and their energy contribution
Tracks
- Track types
- Working with tracks
- Track lists
- Retrieving reference data tracks
- Merge Annotation Tracks
- Merge Variant Tracks
- Track Conversion
  - Convert to Tracks
  - Convert from Tracks
- Annotate and Filter
- Graphs
Prepare sequencing data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
Quality control for resequencing analysis
- QC for Targeted Sequencing
- QC for Read Mapping
- Whole Genome Coverage Analysis
- Combine Reports
  - Combine Reports output
  - Report types supported
- Create Sample Report
  - Create Sample Report output
Read mapping
- Map Reads to Reference
- Reads tracks and stand-alone read mappings
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
  - Algorithm details and parameters
  - Running the duplicate reads removal
- Extract Consensus Sequence
Variant detection
- Variant Detection tools
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detection - filters
  - General filters
  - Noise filters
- Variant Detection - the outputs
- Fixed Ploidy and Low Frequency Detection tools: detailed descriptions
- Copy Number Variant Detection
- Identify Known Mutations from Sample Mappings
  - Run the Identify Known Mutations from Sample Mappings tool
  - Output from the Identify Known Mutations from Sample Mappings tool
- InDels and Structural Variants
Resequencing analysis
- Variant filtering
- Variant annotation
- Variants comparison
- Variant quality control
  - Create Variant Track Statistics Report
- Functional consequences
RNA-seq and Small RNA analysis
- RNA-seq normalization
- RNA-Seq Analysis
- PCA for RNA-Seq
  - Principal component analysis plot (2D)
  - Principal component analysis plot (3D)
- Differential Expression
- Create Heat Map for RNA-Seq
  - Clustering of features and samples
  - The heat map view
- Create Expression Browser
  - The expression browser
- Create Venn Diagram for RNA-Seq
  - Venn diagram table view
- Gene Set Test
  - Tool output and GAF file comparison
- miRNA analysis
Microarray analysis
- Experimental design
- Transformation and normalization
- Quality control
- Feature clustering
  - Hierarchical clustering of features
  - K-means/medoids clustering
- Statistical analysis - identifying differential expression
- Annotation tests
  - Hypergeometric Tests on Annotations
  - Gene Set Enrichment Analysis
- General plots
De Novo sequencing
- The CLC de novo assembly algorithm
- De Novo Assembly
- Map Reads to Contigs
Epigenomics analysis
- Histone Chip-Seq
- ChIP-Seq Analysis
- Annotate with nearby gene information
- Bisulfite Sequencing
- Advanced Peak Shape Tools
Utility tools
- Batch Rename
- Extract Annotations
- Sample reads
- Extract Reads
- Merge Overlapping Pairs
Legacy tools
- Compare Sample Variant Tracks
- Remove Reference Variants
- Import Roche 454
- Create Combined RNA-Seq Report
- Create Track from Experiment
- Small RNA Analysis
- Batch launching workflows with multiple inputs
Appendix
- Use of multi-core computers
- Graph preferences
- BLAST databases
- Proteolytic cleavage enzymes
- Restriction enzymes database configuration
- Technical information about modifying Gateway cloning sites
- IUPAC codes for amino acids
- IUPAC codes for nucleotides
- Formats for import and export
  - List of bioinformatic data formats
  - List of graphics data formats
- SAM/BAM export format specification
  - Flags
- Gene expression annotation files and microarray data formats
- Translation Tables
- Custom codon frequency tables
- Comparison of track comparison tools
- Matrices for alignment calculation
Bibliography

Viewing mode

Using a CLC Workbench in Viewing Mode is a free and easy way to access extensive data viewing capabilities, basic bioinformatics analysis tools, as well as import and export functionality.

Data viewing

Any data type supported by the Workbench being used can be viewed in Viewing Mode. Plugins or modules can also be installed when in Viewing Mode, expanding the range of data types supported.

Viewing Mode of the CLC Workbenches can be particularly useful when sharing data with colleagues or reviewers who wish to view and investigate data you have generated but who do not have access to a Workbench license.

Data import, export and analysis in Viewing Mode

When working in Viewing Mode, the Import and Export buttons in the top Toolbar are enabled, and standard import and export functionality for many bioinformatics data types is supported. Tools available can be seen in the Workbench Toolbox, as illustrated in figure 1.21.

Image viewing_mode_toolbox
Figure 1.21: Bioinformatics tools available when using Viewing Mode are found in the Toolbox.

Starting a CLC Workbench in Viewing Mode

A button labeled Viewing Mode is presented in the Workbench License Manager when a Workbench is started up without a license installed, as shown in figure 1.22. This button is also visible in message windows that appear if a Workbench is started up that has an expired license or that is configured to use a network license but all the available licenses have been checked out by others, as described in Common issues when using a network license.

Click on the Viewing Mode button to start up the Workbench in Viewing Mode.

Image viewing_mode_button1
Figure 1.22: Click on the Viewing Mode button at the bottom of the License Manager window to launch the Workbench in Viewing Mode.

To go from running in Viewing Mode to running a Workbench with its full functionality, it just needs to have access to a valid license. This can be done by installing a static license, or when using a network license, by restarting the Workbench when licenses are once again available.