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• Introduction to CLC Genomics Workbench
  • Contact information and citation
  • Download and installation
    • Installation on Microsoft Windows
    • Installation on macOS
    • 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 manager connection
    • Download a static license on a non-networked machine
    • Viewing mode
    • Start in safe mode
  • Plugins
    • Install
    • Uninstall
    • Updating plugins
  • Network configuration
  • History of the CLC Workbenches
• User interface
  • View Area
    • Close views
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Moving a view to a different screen
    • Side Panel
  • Zoom functionality in the View Area
  • Toolbox and Favorites tabs
    • Toolbox tab
    • Favorites tab
  • Processes tab and Status bar
  • History and Element Info views
  • 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
  • Working with tables
    • Filtering tables
  • Customized attributes on data locations
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching custom attributes
  • Searching for data in CLC Locations
    • Quick Search
    • Local Search
• User preferences and settings
  • General preferences
  • View preferences
    • Import and export Side Panel settings
  • Data preferences
  • Advanced preferences
  • Export/import of preferences
  • Side Panel view settings
• Printing
  • Selecting which part of the view to print
  • Page setup
  • Print preview
• Connections to other systems
  • CLC Server connection
  • AWS Connections
• Import/export of data and graphics
  • Standard import
    • External files
  • Import tracks
    • GFF3 format
    • VCF import
  • Import high-throughput sequencing data
    • Illumina
    • PacBio
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent
    • MGI/BGI
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Import RNA spike-in controls
  • Import Primers
    • Import Primer Pairs
  • Data export
    • Export formats
    • Export parameters
    • Specifying the exported file name(s)
    • Export of folders and data elements in CLC format
    • Export of dependent elements
    • Export of tables
    • Export in VCF format
    • GFF3 export
    • JSON export
    • Graphics export
    • Export history
    • Backing up data from the CLC Workbench
  • 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
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
    • UniProt search options
    • Handling of UniProt search results
  • Search for Reads in SRA
    • Searching SRA
    • Downloading reads and metadata from SRA
    • Troubleshooting SRA downloads
  • Sequence web info
• References management
  • Download Genomes
  • QIAGEN Sets
  • Custom Sets
    • Copy to References
    • Export a Custom Data Set
    • Import a Custom Data Set
  • Imported Data
  • Exporting reference data outside of the Reference Data Manager framework
• Running tools, handling results and batching
  • Running tools
    • Running a tool on a CLC Server
  • Handling results
  • 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
    • Finding data elements based on metadata
    • Viewing metadata associations
    • Removing metadata associations
    • Identifying metadata rows without associated data
    • Editing Metadata tables
  • Moving, copying and exporting metadata
• Workflows
  • Creating and editing workflows
    • Adding elements to a workflow
    • Connecting workflow elements
    • Ordering inputs
    • Validating a workflow
    • Viewing the flow of elements in a workflow
    • Adjusting the workflow layout
    • The Configuration Editor view
    • Snippets in workflows
    • Customizing the Workflow Editor
  • Workflow elements
    • Anatomy of workflow elements
    • Basic configuration of workflow elements
    • Configuring input and output elements
    • Control flow elements
    • Track lists as workflow outputs
    • Input modifying tools
  • Launching workflows individually and in batches
    • Workflow Result Metadata tables
    • Running workflows in batch mode
    • Running part of a workflow multiple times
  • Advanced workflow batching
    • Batching workflows with more than one input changing per run
    • Multiple levels of batching
  • Template workflows
    • Import with Metadata
    • Prepare Raw Data
    • Identify DNA Germline Variants workflow
    • RNA-Seq and Differential Gene Expression Analysis workflow
  • Managing workflows
    • Updating workflows
    • Creating a workflow installation file
    • Installing a workflow
• Viewing and editing sequences
  • Sequence Lists
    • Creating sequence lists
    • Graphical view of sequence lists
    • Table view of sequence lists
    • Annotation Table view of sequence lists
    • Working with paired sequences in lists
  • View sequences
    • Sequence settings in Side Panel
    • Selecting parts of the sequence
    • Editing the sequence
    • Sequence region types
    • Circular DNA
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Editing annotations
    • Export annotations to a gff3 format file
    • Removing annotations
  • Element information
  • View as text
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST against local data
  • 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
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Where can I get the BLAST+ programs
    • 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
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Tools for linking sequence and structure
    • Show sequence associated with molecule
    • Link sequence or sequence alignment to structure
    • Transfer annotations between sequence and structure
  • Align Protein Structure
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
  • Generate Biomolecule
• General sequence analyses
  • Annotate with GFF/GTF/GVF file
  • Extract sequences
  • Shuffle sequence
  • Dot plots
    • Create dot plots
    • View dot plots
    • Bioinformatics explained: Dot plots
    • Bioinformatics explained: 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
  • 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
    • When a single primer region is defined
    • When both forward and reverse regions are defined
    • Standard PCR output table
  • Nested PCR
  • TaqMan
  • Sequencing primers
  • 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
    • 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 reads from a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
  • Extract Consensus Sequence
  • Combine Reports
    • Combine Reports output
• Cutting and cloning
  • Restriction site analyses
    • Dynamic restriction sites
    • Restriction Site Analysis
    • Insert restriction site
  • Restriction enzyme lists
  • Restriction Based Cloning
    • Introduction to the Cloning Editor
    • The restriction cloning workflow
    • Manual cloning
  • Homology Based Cloning
    • Working with homology based cloning
    • Adjust the homology based cloning design
    • Homology Based Cloning outputs
    • Detailed description of the Homology Based Cloning wizard
    • Working with mutations
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Gel electrophoresis
    • Gel view
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • 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
    • 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
    • Secondary structure prediction parameters
    • 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
• Tracks
  • Track types
  • Working with tracks
    • Visualizing, zooming and navigating tracks
    • Showing a track in a table
    • The Chromosome Table view
    • Finding annotations on the genome
    • Extract sequences from tracks
  • Track lists
  • Retrieving reference data tracks
  • Merge Annotation Tracks
  • Merge Variant Tracks
  • Track Conversion
    • Convert to Tracks
    • Convert from Tracks
  • Annotate and Filter
    • Annotate with Exon Numbers
    • Annotate with Overlap Information
    • Filter Annotations on Name
    • Filter Based on Overlap
  • Graphs
    • Create GC Content Graph
    • Create Mapping Graph
    • Identify Graph Threshold Areas
• Prepare sequencing data
  • QC for Sequencing Reads
    • Per-sequence analysis
    • Per-base analysis
    • Over-representation analyses
  • Trim Reads
    • Quality trimming
    • Adapter trimming
    • Trim adapter list
    • Homopolymer trimming
    • Sequence trimming
    • Sequence filtering
    • Trim output
  • Demultiplex Reads
    • Demultiplexing single reads
    • Demultiplexing paired reads
    • Entering barcodes
    • Demultiplexing output options
    • Running Demultiplex Reads in workflows
• Quality control for resequencing analysis
  • QC for Targeted Sequencing
    • Coverage summary report
    • Per-region statistics
    • Coverage table
    • Coverage graph
    • Gene coverage
  • Target Region Coverage Analysis
    • Output from Target Region Coverage Analysis
  • QC for Read Mapping
    • References
    • Mapped read statistics
    • Statistics table for each mapping
  • Whole Genome Coverage Analysis
  • Combine Reports
    • Combine Reports output
    • Report types supported
  • Create Sample Report
    • Create Sample Report output
• Read mapping
  • Map Reads to Reference
    • Selecting the reads
    • References and masking
    • Mapping parameters
    • Mapping paired reads
    • Non-specific matches
    • Gap placement
    • Mapping computational requirements
    • Reference caching
    • Mapping output options
    • Summary mapping report
  • Reads tracks and stand-alone read mappings
    • Coloring of mapped reads
    • Reads tracks
    • Stand-alone read mapping
  • Local Realignment
    • Method
    • Realignment of unaligned ends
    • Guided realignment
    • Multi-pass local realignment
    • Known limitations
    • Computational requirements
    • Run the Local Realignment tool
  • Merge Read Mappings
  • Remove Duplicate Mapped Reads
    • Algorithm details and parameters
    • Running remove duplicate mapped reads
  • Extract Consensus Sequence
• Variant detection
  • Variant Detection tools
    • Differences in the variants called by the different tools
    • How the variant detection tools work
    • Detailed information about overlapping paired reads
  • Fixed Ploidy Variant Detection
  • Low Frequency Variant Detection
  • Basic Variant Detection
  • Variant Detection - filters
    • General filters
    • Noise filters
  • Variant Detection - the outputs
    • Variant tracks
    • The annotated variant table
    • The variant detection report
  • Fixed Ploidy and Low Frequency Detection tools: detailed descriptions
    • Variant Detection - error model estimation
    • The Fixed Ploidy Variant Detection tool: Models and methods
    • The Low Frequency Variant Detection tool: Models and methods
  • Copy Number Variant Detection
    • The Copy Number Variant Detection tool
    • Region-level CNV track (Region CNVs)
    • Target-level CNV track (Target CNVs)
    • Gene-level annotation track (Gene CNVs)
    • CNV results report
    • CNV algorithm report
  • 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
    • Run the InDels and Structural Variants tool
    • The Structural Variants and InDels output
    • The InDels and Structural Variants detection algorithm
    • Theoretically expected structural variant signatures
    • How sequence complexity is calculated
• Resequencing analysis
  • Variant filtering
    • Filter against Known Variants
    • Remove Marginal Variants
    • Remove Homozygous Reference Variants
    • Remove Variants Present in Control Reads
  • Variant annotation
    • Annotate from Known Variants
    • Remove Information from Variants
    • Annotate with Effect Scores
    • Annotate with Conservation Score
    • Annotate with Flanking Sequence
    • Annotate with Repeat and Homopolymer Information
  • Variants comparison
    • Identify Shared Variants
    • Identify Enriched Variants in Case vs Control Samples
    • Trio Analysis
  • Variant quality control
    • Create Variant Track Statistics Report
  • Functional consequences
    • Amino Acid Changes
    • Predict Splice Site Effect
    • GO Enrichment Analysis
    • Download 3D Protein Structure Database
    • Link Variants to 3D Protein Structure
  • Create Consensus Sequences from Variants
• RNA-Seq and Small RNA analysis
  • RNA-Seq normalization
  • Create Expression Browser
    • The expression browser
    • Expression browser plot
  • miRNA analysis
    • Quantify miRNA
    • Annotate with RNAcentral Accession Numbers
    • Create Combined miRNA Report
    • Extract IsomiR Counts
    • Explore Novel miRNAs
  • RNA-Seq Tools
    • RNA-Seq Analysis
    • Detect and Refine Fusion Genes
  • Expression Plots
    • PCA for RNA-Seq
    • Create Heat Map for RNA-Seq
    • Create K-medoids Clustering for RNA-Seq
  • Differential Expression
    • Pre-filtering data for Differential Expression
    • The GLM model
    • Differential Expression in Two Groups
    • Differential Expression for RNA-Seq
    • Create Venn Diagram for RNA-Seq
    • Gene Set Test
• Microarray analysis
  • Experimental design
    • Setting up a microarray experiment
    • Organization of the experiment table
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Create Box Plot
    • Hierarchical Clustering of Samples
    • Principal Component Analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Statistical analysis - identifying differential expression
    • Tests on proportions
    • Gaussian-based tests
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Annotation tests
    • Hypergeometric Tests on Annotations
    • Gene Set Enrichment Analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• De Novo sequencing
  • The CLC de novo assembly algorithm
    • 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
  • De Novo Assembly
    • Best practices
    • Randomness in the results
    • De novo assembly parameters
    • De novo assembly report
    • De novo assembly output
  • Map Reads to Contigs
• Epigenomics analysis
  • Histone Chip-Seq
  • 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
    • Peak track
  • Annotate with nearby gene information
  • Bisulfite Sequencing
    • Detecting DNA methylation
    • Map Bisulfite Reads to Reference
    • Call Methylation Levels
    • Create RRBS-fragment Track
  • Advanced Peak Shape Tools
    • Learn Peak Shape Filter
    • Apply Peak Shape Filter
    • Score Regions
• Utility tools
  • Extract Annotated Regions
  • Extract Reads
  • Filter on Custom Criteria
  • Merge Overlapping Pairs
  • Track tools
  • Create Sequence List
  • Update Sequence Attributes in Lists
  • Split Sequence List
  • Subsample Sequence List
  • Rename Elements
  • Rename Sequences in Lists
• Legacy tools
  • QIAGEN GeneReader Sequencing Import (legacy)
• Appendix
  • 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

Project settings

A number of general settings can be adjusted from the Side Panel. Personal settings as well as molecule visualizations can be saved by clicking in the lower right corner of the Side Panel (). This is described in detail in Side Panel view settings.

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Subsections

• Project Tree Tools
• Property viewer
• Visualization settings

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