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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 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
- Handling results
  - Running a tool on a CLC Server
- 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
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
  - Visualizing, zooming and navigating tracks
  - Showing a track in a table
- Track lists
- Retrieving reference data tracks
- Merge Annotation 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
  - Report types supported
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
- Reverse sequence
- 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
- 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

CLC Server connection

Using a CLC Server, data can be stored centrally and analyses run on a central machine rather than on a personal computer. After logging into the CLC Server from a Workbench, data in CLC Server locations will be listed in the Workbench Navigation Area. When launching analyses that can be run on the CLC Server, you will be offered the choice of running them using the Workbench or the CLC Server.

To log into a CLC Server or to check on the status of an existing connection, go to:

File | CLC Server Connection ()

This will bring up a login dialog as shown in figure 1.27.

Image serverlogin1
Figure 1.27: The CLC Server Connection dialog.

To log into a CLC Server, fill in the text fields. Your server administrator should be able to provide you with the necessary details. When you click on the Log In button, the Workbench will connect to the CLC Server if your credentials are accepted.

Your username and the server details will be saved between Workbench sessions. If you wish your password to be saved also, click in the box beside the Remember password box.

If you wish the Workbench to connect to the server automatically on startup, then check the box beside the option Log into CLC Server at Workbench startup. This option is only enabled when the Remember password option has been selected.

Further information about working with a CLC Server from a CLC Workbench is available in this manual:

Launching tasks on a CLC Server is described in Running a tool on a CLC Server.
Monitoring processes sent to the CLC Server from a CLC Workbench is described in Toolbox and Status Bar.
Viewing and working with data held on a CLC Server is described in Data structure, and deleting data held on a CLC Server is described in Delete, restore and remove elements.
Importing data to a CLC Server and exporting data held on a CLC Server is described in CLC Server data import and export.

For those logging into the CLC Server as a user with administrative privileges, an option called Manage Server Users and Groups... will be available. This is described in detail at http://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=User_authentication_using_Workbench.html.