• Manuals

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• Introduction to CLC Genomics Workbench
  • Contact information
  • Download and installation
    • Program download
    • Installation on Microsoft Windows
    • Installation on Mac OS X
    • Installation on Linux with an installer
  • System requirements
    • Limitations on maximum number of cores
  • Workbench Licenses
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Upgrade license
    • Configure license server connection
    • Download a static license on a non-networked machine
    • Limited mode
  • About CLC Workbenches
    • New program feature request
    • Getting help
    • CLC Sequence Viewer vs. Workbenches
  • When the program is installed: Getting started
    • Quick start
    • Import of example data
  • Plugins
    • Installing plugins
    • Uninstalling plugins
    • Updating plugins
  • Network configuration
  • Latest improvements
• User interface
  • View Area
    • Open view
    • Open additional views with the toolbar
    • Close views
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Moving a view to a different screen
    • Side Panel
  • Zoom and selection in View Area
    • Zoom in
    • Zoom out
    • Selecting, panning and zooming
  • Toolbox and Status Bar
    • Processes
    • Toolbox
    • Status Bar
  • Workspace
    • Create Workspace
    • Select Workspace
    • Delete Workspace
  • List of shortcuts
• Data management and search
  • Navigation Area
    • Data structure
    • Create new folders
    • Sorting folders
    • Multiselecting elements
    • Moving and copying elements
    • Change element names
    • Delete, restore and remove elements
    • Show folder elements in a table
  • Metadata
    • Importing Metadata
    • Associating data elements with metadata
    • Working with data and metadata
  • Working with tables
    • Filtering tables
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
  • Local search
    • What kind of information can be searched?
    • Quick search
    • Advanced search
    • Search index
• 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 using the import dialog
    • Import using drag and drop
    • Import using copy/paste of text
    • External files
  • Import tracks
  • Import high-throughput sequencing data
    • Roche 454
    • Illumina
    • SOLiD
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent
    • Complete Genomics
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Data export
    • Export of folders and multiple elements in CLC format
    • Export of dependent elements
    • Export history
    • The CLC format
    • Backing up data from the CLC Workbench
    • Export of workflow output
    • Export of tables
  • Export graphics to files
    • Which part of the view to export
    • Save location and file formats
    • Graphics export parameters
    • Exporting protein reports
  • Export graph data points to a file
  • Copy/paste view output
• Running tools, handling results and batching
  • Running tools
  • Handling results
  • Batch processing
    • Standard batch processing
    • Batch overview
    • Parameters for batch runs
    • Running the analysis and organizing the results
    • Batch launching workflows with multiple inputs
• Workflows
  • Creating a workflow
    • Adding workflow elements
    • Configuring workflow elements
    • Locking and unlocking parameters
    • Connecting workflow elements
    • Input and output
    • Layout
    • Input modifying tools
    • Workflow validation
    • Workflow creation helper tools
    • Adding to workflows
    • Snippets in workflows
    • Change the order of tracks in the Genome Browser View
  • Distributing and installing workflows
    • Creating a workflow installation file
    • Installing a workflow
    • Managing workflows
    • Workflow identification and versioning
    • Automatic update of workflow elements
  • Executing a workflow
  • Open copy of installed workflow
• Viewing and editing sequences
  • View sequence
    • Sequence settings in Side Panel
    • Selecting parts of the sequence
    • Editing the sequence
    • Sequence region types
  • Circular DNA
    • Using split views to see details of the circular molecule
    • Mark molecule as circular and specify starting point
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Edit annotations
    • Removing annotations
  • Element information
  • View as text
  • Sequence Lists
    • Graphical view of sequence lists
    • Sequence list table
    • Extract sequences from sequence list
• Data download
  • GenBank search
    • GenBank search options
    • Handling of GenBank search results
    • Save GenBank search parameters
  • UniProt (Swiss-Prot/TrEMBL) search
    • UniProt search options
    • Handling of UniProt search results
    • Save UniProt search parameters
  • Search for structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Download reference genome data
    • Selecting data types for download
    • Cytogenetic ideograms
  • Sequence web info
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST a partial sequence against NCBI
    • BLAST against local data
    • BLAST a partial sequence against a local database
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST HSP table
    • BLAST hit table
    • Extracting a consensus sequence from a BLAST result
  • Local BLAST databases
    • Make pre-formatted BLAST databases available
    • Download NCBI pre-formatted BLAST databases
    • Create local BLAST databases
  • Manage BLAST databases
  • Bioinformatics explained: BLAST
    • Examples of BLAST usage
    • Searching for homology
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Explanation of the BLAST output
    • I want to BLAST against my own sequence database, is this possible?
    • What you cannot get out of BLAST
    • Other useful resources
• 3D Molecule Viewer
  • Importing molecule structure files
    • From the Protein Data Bank
    • From your own file system
    • BLAST search against the PDB database
    • Import issues
  • Viewing molecular structures in 3D
    • Moving and rotating
    • Troubleshooting 3D graphics errors
    • Updating old structure files
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Snapshots of the molecule visualization
  • Tools for linking sequence and structure
    • Show sequence associated with molecule
    • Link sequence or sequence alignment to structure
    • Transfer annotations between sequence and structure
  • Protein structure alignment
    • The Align Protein Structure dialog box
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
• 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
    • Dynamic motifs
    • Motif search from the Toolbox
    • Java regular expressions
  • 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
    • Why the interest in signal peptides?
    • Different types of signal peptides
    • Prediction of signal peptides and subcellular localization
    • The SignalP method
    • What do the SignalP scores mean?
  • 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
    • Saving primers
    • Saving PCR fragments
    • Adding primer binding annotation
  • 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
    • Specific options for alignment-based primer and probe design
    • Alignment based design of PCR primers
    • Alignment-based TaqMan 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
    • View settings in the Side Panel
    • Editing a contig or read mapping
    • Sorting reads
    • Read conflicts
    • Using the mapping
    • Extract parts of a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
• Cloning and cutting
  • Molecular cloning
    • Introduction to the cloning editor
    • The cloning workflow
    • Manual cloning
    • Insert restriction site
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Restriction site analysis
    • Dynamic restriction sites
    • Restriction site analysis from the Toolbox
  • Gel electrophoresis
    • Separate fragments of sequences on gel
    • Separate sequences on gel
    • Gel view
  • Restriction enzyme lists
    • Create enzyme list
    • View and modify enzyme list
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
  • Bioinformatics explained: Sequence logo
    • Calculation of sequence logos
  • Edit alignments
    • Move residues and gaps
    • Insert gaps
    • Delete residues and gaps
    • Copy annotations to other sequences
    • Move sequences up and down
    • Delete, rename and add sequences
    • Realign selection
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
  • Bioinformatics explained: Multiple alignments
    • Use of multiple alignments
    • Constructing multiple alignments
• Phylogenetic trees
  • Phylogenetic tree features
  • Create Trees
    • K-mer Based Tree Construction
    • Create tree
    • Model Testing
    • Maximum Likelihood Phylogeny
    • Bioinformatics explained
  • Tree Settings
    • Minimap
    • Tree layout
    • Node settings
    • Label settings
    • Background settings
    • Branch layout
    • Bootstrap settings
    • Visualizing metadata
    • Node right click menu
  • Metadata and phylogenetic trees
    • Table Settings and Filtering
    • Add or modify metadata on a tree
    • Undefined metadata values on a tree
    • Selection of specific nodes
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Structure output
    • Partition function
    • Advanced options
    • Structure as annotation
  • View and edit secondary structures
    • Graphical view and editing of secondary structure
    • Tabular view of structures and energy contributions
    • Symbolic representation in sequence view
    • Probability-based coloring
  • 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
    • Quality trimming
    • Adapter trimming
    • Length trimming
    • Trim output
  • Demultiplex reads
  • Sequencing data quality control
    • Qc Sequencing Report Content
    • Adapters
    • Running the quality control tool
  • Merge overlapping pairs
    • Using quality scores when merging
    • Report of merged pairs
• Tracks
  • Track lists
    • Zooming and navigating track views
    • Adding, removing and reordering tracks
    • Showing a track in a table
    • Open track from a track list in table view
    • Finding annotations on the genome
    • Extract sequences from tracks
    • Creating track lists in workflows
  • Retrieving reference data tracks
  • Merging tracks
  • Converting data to tracks and back
    • Convert to tracks
    • Convert from tracks
  • Annotate and filter tracks
    • Annotate with overlap information
    • Extract reads based on overlap
    • Filter annotations on name
    • Filter Based on Overlap
  • Graphs
    • Create GC Content Graph
    • Create Mapping Graph
    • Identify Graph Threshold Areas
• Read mapping
  • Map Reads to Reference
    • Selecting reads and reference
    • Including or excluding regions (masking)
    • Mapping parameters
    • Mapping paired reads
    • Non-specific matches
    • Gap placement
    • Computational requirements
    • Reference Caching
  • Mapping output
    • Mapping output options
    • Mapped reads coloring
    • Reads track output from a read mapping
    • Stand-alone read mapping
    • Mapping table
    • View settings in the Side Panel
    • Overlapping paired reads
    • Find broken pair mates
  • Mapping reports
    • Summary mapping report
    • Detailed mapping report
  • Mapping SOLid reads in color space
    • Viewing color space information
    • Mapping in color space
  • Local realignment
    • Method
    • Realignment of unaligned ends
    • Guided Realignment
    • Multi-pass local realignment
    • Known Limitations
    • Computational Requirements
    • How to run the Local Realignment tool
  • 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
    • Running the Create Statistics for Target Regions
    • Coverage summary report
    • Per-region statistics
    • Coverage table
    • Coverage graph
  • InDels and Structural Variants
    • How to run the InDels and Structural Variants tool
    • The Structural Variants and InDels output
    • The InDels and Structural Variants detection algorithm
    • The InDels and Structural Variants detection algorithm - Step 1: Creating Left- and Right breakpoint signatures
    • The InDels and Structural Variants detection algorithm - Step 2: Creating Structural variant signatures
    • Theoretically expected structural variant signatures
    • How sequence complexity is calculated
  • 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 variant track output
    • The annotated table output
    • The report
  • 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
    • Variant tracks
    • The annotated variant table
    • Variant types
  • Detailed information about overlapping paired reads
  • Annotate and filter variants
    • Filter against known variants
    • Annotating from known variants
    • Annotate with exon numbers
    • Annotate with flanking sequence
    • Filter marginal variant calls
    • Filter reference variants
  • Comparing variants
    • Compare variants within group
    • Compare sample variants
    • Fisher exact test
    • Trio analysis
    • Filter Against Control Reads
  • Predicting functional consequences
    • Amino acid changes
    • Predict splice site effect
    • GO enrichment analysis
    • Conservation score annotation
    • Link Variants to 3D Protein Structure
    • Download 3D Protein Structure Database
• Transcriptomics
  • RNA-Seq analysis
    • Specifying reads and reference
    • Tightly packed genes and genes in operons
    • Defining mapping options for RNA-Seq
    • Calculating expression values from RNA-Seq
    • Specifying RNA-Seq outputs
    • Interpreting the RNA-Seq analysis result
  • Small RNA analysis
    • Extract and count
    • Downloading miRBase
    • Annotating and merging small RNA samples
    • Working with the small RNA sample
    • Exploring novel miRNAs
  • Expression profiling by tags
    • Extract and count tags
    • Create virtual tag list
    • Annotate tag experiment
  • Experimental design
    • Setting up an experiment
    • Organization of the experiment table
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Working with tracks and experiments
    • Data structures for transcriptomics
    • From Experiments to Tracks
    • Running the Create Track from Experiment tool
    • Interpreting the results of the Create Track from Experiment tool
    • Visualizing RNA-Seq read tracks for the experiment
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Creating box plots - analyzing distributions
    • Hierarchical clustering of samples
    • Principal component analysis
  • Statistical analysis - identifying differential expression
    • Empirical analysis of DGE
    • Tests on proportions
    • Gaussian-based tests
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Annotation tests
    • Hypergeometric tests on annotations
    • Gene set enrichment analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• De novo sequencing
  • De novo assembly
    • How it works
    • Resolve repeats using reads
    • Automatic paired distance estimation
    • Optimization of the graph using paired reads
    • AGP export
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
    • Randomness in the results
    • SOLiD data support in de novo assembly
    • De novo assembly parameters
    • De novo assembly report
  • Map reads to contigs
• Epigenomics
  • ChIP-Seq Analysis
    • Quality Control of ChIP-Seq data
    • Learning peak shapes
    • Applying peak shape filters to call peaks
    • Running the Transcription Factor ChIP-Seq tool
  • Annotate with nearby gene information
• Legacy tools
  • Quality-based variant detection
    • Assessing the quality of the neighborhood bases
    • Significance of variant
    • Ploidy and genetic code
    • Reporting the variants
  • Probabilistic variant detection
    • Calculation of the prior and error probabilities
    • Calculation of the likelihood
    • Calculation of the posterior probability for each site type at each position in the genome
    • Comparison with the reference sequence and identification of candidate variants
    • Posterior filtering and reporting of variants
    • Running the variant detection
    • Setting ploidy and genetic code
    • Reporting the variants found
  • 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
    • Peptide sequence databases
    • Nucleotide sequence databases
    • Adding more 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
    • GEO (Gene Expression Omnibus)
    • Affymetrix GeneChip
    • Illumina BeadChip
    • Gene ontology annotation files
    • Generic expression and annotation data file formats
  • Translation Tables
    • 1. Standard
    • 2. Vertebrate Mitochondrial
    • 3. Yeast Mitochondrial
    • 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
    • 5. Invertebrate Mitochondrial
    • 6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
    • 9. Echinoderm Mitochondrial; Flatworm Mitochondrial
    • 10. Euplotid Nuclear
    • 11. Bacterial and Plant Plastid
    • 12. Alternative Yeast Nuclear
    • 13. Ascidian Mitochondrial
    • 14. Alternative Flatworm Mitochondrial
    • 15. Blepharisma Macronuclear
    • 16. Chlorophycean Mitochondrial
    • 21. Trematode Mitochondrial
    • 22. Scenedesmus Obliquus Mitochondrial
    • 23. Thraustochytrium Mitochondrial
    • 24. Pterobranchia Mitochondrial
    • 25. Candidate Division SR1 and Gracilibacteria
  • Custom codon frequency tables
  • Comparison of track comparison tools
  • Matrices for alignment calculation
    • PAM30 log-odds matrix
    • PAM60 log-odds matrix
    • BLOSUM42 log-odds matrix
    • BLOSUM62 log-odds matrix
    • BLOSUM80 log-odds matrix
• Bibliography

System requirements

• Windows Vista, Windows 7, Windows 8, Windows 10, Windows Server 2008, or Windows Server 2012
• Mac OS X 10.7 or later
• Linux: RHEL 5.0 or later. SUSE 10.2 or later. Fedora 6 or later
• 2 GB RAM required
• 4 GB RAM recommended
• 1024 x 768 display required
• 1600 x 1200 display recommended
• Intel or AMD CPU required

• Special requirements for the 3D Molecule Viewer System requirements
  • A graphics card capable of supporting OpenGL 2.0.
  • Updated graphics drivers. Please make sure the latest driver for the graphics card is installed .

  System Recommendations

  • A discrete graphics card from either Nvidia or AMD/ATI. Modern integrated graphics cards (such as the Intel HD Graphics series) may also be used, but these are usually slower than the discrete cards.
  • A 64-bit workbench version is recommended for working with large complexes.

• Special requirements for read mapping. The numbers below give minimum and recommended memory for systems running mapping and analysis tasks. The requirements suggested are based on the genome size.
  • E. coli K12 (4.6 megabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • C. elegans (100 megabases) and Arabidopsis thaliana (120 megabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • Zebrafish (1.5 gigabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • Human (3.2 gigabases) and Mouse (2.7 gigabases)
    • Minimum: 6 GB RAM
    • Recommended: 8 GB RAM

• Special requirements for de novo assembly. De novo assembly may need more memory than stated above - this depends both on the number of reads, error profile and the complexity and size of the genome. See http://www.clcbio.com/white-paper for examples of the memory usage of various data sets.
  • 64 bit computer and operating system required to use more than 2 GB RAM.

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Subsections

• Limitations on maximum number of cores

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