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Introduction to CLC Genomics Workbench
- Contact information
- System requirements
  - Limitations on maximum number of cores
- Licenses
- About CLC Workbenches
- When the program is installed: Getting started
  - Quick start
  - Import of example data
- Plug-ins
- 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
- Customized attributes on data locations
- Filling in values
  - What happens when the sequence is copied to another data location?
  - Searching
- Local search
User preferences and settings
- General preferences
- Default view preferences
  - Number formatting in tables
  - 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
  - Floating Side Panel
Printing
- Selecting which part of the view to print
- Page setup
  - Header and footer
- Print preview
Import/export of data and graphics
- Standard import
- Import high-throughput sequencing data
- Import tracks
- Data export
- Export graphics to files
- Export graph data points to a file
- Copy/paste view output
History log
- Element history
  - Sharing data with history
Batching and result handling
- Batch processing
- How to handle results of analyses
  - Table outputs
  - Batch log
Workflows
- Creating a workflow
- Distributing and installing workflows
- Executing a 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
- Creating a new sequence
- Sequence Lists
Data download
- GenBank search
- UniProt (Swiss-Prot/TrEMBL) search
- Search for structures at NCBI
- Download reference genome
  - Selecting data types for download
- Sequence web info
BLAST search
- Running BLAST searches
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
  - Migrating from a previous version of the Workbench
- Bioinformatics explained: BLAST
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
  - Moving and rotating
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Snapshots of the molecule visualization
- Sequences associated with the molecules
- Troubleshooting 3D graphics errors
- Updating old structure files
General sequence analyses
- 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
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
  - Pfam search parameters
  - Download and installation of additional Pfam databases
- 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
  - Manual trimming
  - Automatic trimming
- Assemble sequences
- Assemble sequences to reference
- Add sequences to an existing contig
- View and edit 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
- Inferring phylogenetic trees
  - Phylogenetic tree parameters
- Maximum Likelihood Phylogeny
  - Tree View Preferences
- Bioinformatics explained: phylogenetics
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
- Trimming
- Multiplexing
  - Sort sequences by name
  - Process tagged sequences
- Sequencing data quality control
  - Report contents
  - Running the quality control tool
- 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
- Creating graph tracks
Read mapping
- The read mapper tool
- Mapping reports
  - Detailed mapping report
  - Summary mapping report
- Color space
- Mapping result
- Local realignment
- Merge mapping results
- Extract consensus sequence
- Coverage analysis
  - Running the Coverage analysis tool
Resequencing
- Create Statistics for Target Regions
- Quality-based variant detection
- Probabilistic variant detection
- What is the InDels and Structural Variants tool?
- Variant data
- Detailed information about overlapping paired reads
- Annotate and filter variants
- Comparing variants
- Predicting functional consequences
Transcriptomics
- RNA-Seq analysis
- Expression profiling by tags
- Small RNA analysis
- Experimental design
- 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 sequencing
Appendix
- Comparison of workbenches
- Use of multi-core computers
- Graph preferences
- Working with tables
  - Filtering tables
- 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
- Microarray data formats
- Translation Tables
- Custom codon frequency tables
- Comparison of track comparison tools
- Matrices for alignment calculation
Bibliography

Read mapping formats

File type	Suffix	Import	Export	Description
ACE	.ace	X	X	No chromatogram or quality score
AGP	.agp/.fa		X	Exports scaffolded contigs (see below)
BAM	.bam	X	X	Compressed version of SAM. See SAM import
CLC	.clc	X	X	Rich format including all information
CLC Assembly File	.cas	X		Output from the CLC Assembly Cell
SAM	.sam	X	X	Sequence Alignment/Map. See Sequence assembly files

Special note about AGP format: both sequence lists and contigs with reads mapped can be used. Based on annotations of type Scaffold (which are automatically added when running the de novo assembly with the scaffold option), the contigs are broken up before exported as fasta. The agp file produced holds information about how the contigs relate to each other.