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Introduction to CLC Main Workbench
- Contact information
- Download and installation
- System requirements
- Workbench Licenses
- When the program is installed: Getting started
  - Quick start
- Plugins
- Network configuration
- 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
- Metadata
- 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
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- Copy/paste view output
Data download
- Search for Sequences at NCBI
  - NCBI search options
  - Handling of NCBI search results
- Search for structures at NCBI
- UniProt (Swiss-Prot/TrEMBL) search
- Sequence web info
Running tools, handling results and batching
- Running tools
- Handling results
- Batch processing
Workflows
- Creating a workflow
- Distributing and installing workflows
- Executing a workflow
- Open copy of installed workflow
Other data types
- Tracks
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
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
  - Updating old structure files
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking sequence and structure
- Protein structure alignment
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
General sequence analyses
- Extract Annotations
- 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
- Reverse sequence
- 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
- Pfam domain search
  - Download of Pfam database
  - Running Pfam Domain Search
- Secondary structure prediction
- Protein report
- Reverse translation from protein into DNA
  - Bioinformatics explained: Reverse translation
- Proteolytic cleavage detection
  - Bioinformatics explained: Proteolytic cleavage
Sequencing data analyses and Assembly
- 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
Primers and probes
- 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
Cloning and restriction sites
- Restriction site analyses
  - Dynamic restriction sites
  - Restriction Site Analysis
- Restriction enzyme lists
- Molecular cloning
- Gateway cloning
- Gel electrophoresis
  - Gel view
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
Expression analysis
- Experimental design
- Working with tracks and experiments
  - Data structures for transcriptomics
- Transformation and normalization
- Quality control
- Statistical analysis - identifying differential expression
- Feature clustering
  - Hierarchical clustering of features
  - K-means/medoids clustering
- Annotation tests
  - Hypergeometric tests on annotations
  - Gene set enrichment analysis
- General plots
BLAST search
- Running BLAST searches
  - BLAST at NCBI
  - BLAST against local data
- Output from BLAST searches
- Extract consensus sequence
- Local BLAST databases
- Manage BLAST databases
- Bioinformatics explained: BLAST
Appendix
- 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
- Gene expression annotation files and microarray data formats
- Translation Tables
- Custom codon frequency tables
- Matrices for alignment calculation
Bibliography

Contact information

The CLC Main Workbench is developed by:

QIAGEN Aarhus
Silkeborgvej 2
Prismet
8000 Aarhus C
Denmark

http://www.qiagenbioinformatics.com

Email: AdvancedGenomicsSupport@qiagen.com

The QIAGEN Aarhus team is continuously improving the CLC Main Workbench with our users' interests in mind. We welcome all requests and feedback from users, as well as suggestions for new features or more general improvements to the program.

Getting help via the workbench

If you encounter a problem or need help understanding how the CLC Main Workbench works, and the license you are using is covered by our Maintenance, Upgrades and Support (MUS) program (http://www.qiagenbioinformatics.com/maintenance-and-support/), you can contact our customer support via the workbench by going to the menu option:

Help | Contact Support

This will open a dialog where you can enter your contact information, and a text field for writing the question or problem you have. On a second dialog you will be given the chance to attach screenshots or even small datasets that can help explain or troubleshoot the problem. When you send a support request this way, it will automatically include helpful technical information about your installation and your license information so that you do not have to look this up yourself. Our support staff will reply to you by email.

Other ways to contact the support team

You can also contact the support team by email: AdvancedGenomicsSupport@qiagen.com

Please provide your contact information, your license information, some technical information about your installation , and describe the question or problem you have. You can also attach screenshots or even small data sets that can help explain or troubleshoot the problem.

Information about how to to find your license information is included in the licenses section of our Frequently Asked Questions (FAQ) area: https://secure.clcbio.com/helpspot/index.php?pg=kb. Information about MUS cover on particular licenses can be found by https://secure.clcbio.com/myclc/login.