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Introduction to CLC Genomics Workbench
- Contact information
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- About CLC Workbenches
- When the program is installed: Getting started
  - Quick start
  - Import of example data
- 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
User preferences and settings
- General preferences
- View preferences
  - Import and export Side Panel settings
- Data preferences
- Advanced preferences
  - Default data location
  - NCBI BLAST
- Export/import of preferences
  - The different options for export and import
- View settings for the Side Panel
  - Saving, removing and applying saved settings
Printing
- Selecting which part of the view to print
- Page setup
- Print preview
Import/export of data and graphics
- Standard import
- Import tracks
- Import high-throughput sequencing data
- Data export
- Export graphics to files
- Export graph data points to a file
- Copy/paste view output
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
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
Data download
- GenBank search
- UniProt (Swiss-Prot/TrEMBL) search
- Search for structures at NCBI
- Download reference genome data
  - Selecting data types for download
  - Cytogenetic ideograms
- Sequence web info
BLAST search
- Running BLAST searches
- 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
- Snapshots of the molecule visualization
- Tools for linking sequence and structure
- Protein structure alignment
General sequence analyses
- Extract Annotations
- Extract sequences
- Shuffle sequence
- Dot plots
  - Create dot plots
  - View dot plots
- Bioinformatics explained: Dot plots
  - Realization of dot plots
  - Examples and interpretations of dot plots
- Bioinformatics explained: Scoring matrices
  - Different scoring matrices
  - Use of scoring matrices
- 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
  - Translate part of a nucleotide sequence
- Find open reading frames
  - Open reading frame parameters
Protein analyses
- Signal peptide prediction
  - Signal peptide prediction parameter settings
  - Signal peptide prediction output
- Bioinformatics explained: Prediction of signal peptides
- Protein charge
  - Modifying the layout
- Transmembrane helix prediction
- Antigenicity
  - Plot of antigenicity
  - Antigenicity graphs along sequence
- Hydrophobicity
  - Hydrophobicity plot
  - Hydrophobicity graphs along sequence
- Bioinformatics explained: Protein hydrophobicity
  - Hydrophobicity scales
- Pfam domain search
  - Download of Pfam database
  - Running Pfam Domain Search
- Secondary structure prediction
- Protein report
  - Protein report output
- Reverse translation from protein into DNA
  - Reverse translation parameters
- Bioinformatics explained: Reverse translation
  - The Genetic Code
  - Solving the ambiguities of reverse translation
- Proteolytic cleavage detection
  - Proteolytic cleavage parameters
- 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
  - User input
  - Standard PCR output table
- Nested PCR
  - Nested PCR output table
- TaqMan
  - TaqMan output table
- Sequencing primers
  - Sequencing primers output table
- 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
  - Scaling traces
  - 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
Cloning and cutting
- Molecular cloning
- Gateway cloning
- Restriction site analysis
  - Dynamic restriction sites
  - Restriction site analysis from the Toolbox
- Gel electrophoresis
- Restriction enzyme lists
  - Create enzyme list
  - View and modify enzyme list
Sequence alignment
- Create an alignment
- View alignments
- Bioinformatics explained: Sequence logo
  - Calculation of sequence logos
- Edit alignments
- Join alignments
  - How alignments are joined
- Pairwise comparison
- Bioinformatics explained: Multiple alignments
  - Use of multiple alignments
  - Constructing multiple alignments
Phylogenetic trees
- Phylogenetic tree features
- Create Trees
- 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
Trimming, multiplexing and sequencing quality control
- Trim Sequences
- Demultiplex reads
- Sequencing data quality control
- Merge overlapping pairs
  - Using quality scores when merging
  - Report of merged pairs
Tracks
- Track lists
- Retrieving reference data tracks
- Merging tracks
- Converting data to tracks and back
  - Convert to tracks
  - Convert from tracks
- Annotate and filter tracks
- Graphs
Read mapping
- Map Reads to Reference
- Mapping output
- Mapping reports
  - Summary mapping report
  - Detailed mapping report
- Mapping SOLid reads in color space
  - Viewing color space information
  - Mapping in color space
- Local realignment
- Merge mapping results
- Remove duplicate mapped reads
  - Algorithm details and parameters
  - Running the duplicate reads removal
- Extract consensus sequence
- Sample reads
Resequencing
- Create Statistics for Target Regions
- InDels and Structural Variants
- Coverage analysis
  - Running the Coverage analysis tool
- Variant Detectors - overview
  - Differences in the variants called by the different tools
  - How the variant detection tools work
- Fixed Ploidy Variant Detection
  - Ploidy and sensitivity
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detectors - error model estimation
- Variant Detectors - filters
  - General filters
  - Noise filters
- Variant Detectors - the outputs
- The Fixed Ploidy and Low Frequency variant callers: detailed descriptions
  - The Fixed Ploidy Variant Caller: Models and methods
  - The Low Frequency Variant caller: Models and methods
- Variant data
- Detailed information about overlapping paired reads
- Annotate and filter variants
- Comparing variants
- Predicting functional consequences
Transcriptomics
- RNA-Seq analysis
- Small RNA analysis
- Expression profiling by tags
- Experimental design
- Working with tracks and experiments
- 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
De novo sequencing
- De novo assembly
- Map reads to contigs
Epigenomics
- ChIP-Seq Analysis
- Annotate with nearby gene information
Legacy tools
- Quality-based variant detection
- Probabilistic variant detection
- Special notes about variant callers when upgrading to Genomics Workbench 7.5
Appendix
- Comparison of workbenches
- 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

Running workflows with multiple input elements in batch mode

Workflows with multiple input elements cannot be launched in batch mode using the standard mechanism described in the previous section because extra information is needed to specify the grouping and roles of the data being inupt. This extra information is provided in an Excel format (.xlsx/.xls) file.

Only installed Workflows can be launched in batch mode using the method described in this section. Figures in this section are taken from the Biomedical Genomics Workbench, but the method described will apply to the launching of any Workflow with multiple input elements.

Requirements to be able to launch installed Workflows with multiple inputs using the method described in this section:

All the data elements that will be used as input must be located in a single folder. No input elements in subfolders will be considered.)
An Excel format file (.xlsx/.xls) must be provided. The contents of this file must meet the following criteria:
- The first column must contain the names of the data elements that will be used as inputs.
- At least one other column must be present. That column will contain the grouping information that will specify to the Workbench how to group the data into batch units.

Right click on the name of the Workflow in the Toolbox panel in the bottom left hand side of the Workbench and select the option "Run in Batch Mode...". See figure XXX.
Select the Excel file containing the information about the data to be analysed.
Specify the folder with the data.
The entries in the first column of the Excel sheet will be compared to the names of the data elements in the selected folder. Where the entries and names match perfectly, an icon representing the data type will appear next to the relevant row in the table view within the Wizard.
Click on the button labeled Next.
Specify the column names that will be used to group the data and the type of data each row represents. For example, in an analysis involving three family members, you might group by family and then need to specify whether a given sample of that family is the mother, father or child sample.
Click on the button labeled Next.
The next stage of the Wizard allows you to step through the analysis steps and configure any unlocked paramaters.
Choose where to save the outputs of the analysis.