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Introduction to Biomedical Genomics Workbench
- Contact information
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- When the program is installed: Getting started
- Plugins
- Network configuration
User interface
- View Area
- Zoom and selection in View Area
- Toolbox and Status Bar
- Workspace
- List of shortcuts
Data organization
- 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
- Import tracks
  - GFF3 format
- Import high-throughput sequencing data
- Import RNA spike-in controls
- Import Primer Pairs
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- Copy/paste view output
Data download
- SRA 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 ready-to-use 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
Viewing structures
- Importing molecule structure files
- Viewing molecular structures in 3D
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking sequence and structure
- Protein structure alignment
Ready-to-Use Workflows descriptions and guidelines
- General Workflow
- Somatic Cancer
- Hereditary Disease
Reference data for ready-to-use workflows
- Download and configure reference data
- Create a custom Reference Data Set
- Exporting reference data for use in external applications
- Troubleshooting reference data downloads
Preparing raw data
- Prepare Overlapping Raw Data (not recommended)
- Prepare Raw Data (recommended)
  - Output from the Prepare Raw Data workflow
  - How to check the output reports
Whole genome sequencing (WGS)
- General Workflows (WGS)
  - Annotate Variants (WGS)
  - Identify Known Variants in One Sample (WGS)
- Somatic Cancer (WGS)
- Hereditary Disease (WGS)
Whole exome sequencing (WES)
- General Workflows (WES)
  - Annotate Variants (WES)
  - Identify Known Variants in One Sample (WES)
- Somatic Cancer (WES)
- Hereditary Disease (WES)
Targeted amplicon sequencing (TAS)
- General Workflows (TAS)
  - Annotate Variants (TAS)
  - Identify Known Variants in One Sample (TAS)
- Somatic Cancer (TAS)
- Hereditary Disease (TAS)
Whole Transcriptome Sequencing (WTS)
- Analysis of multiple samples
- Annotate Variants (WTS)
- Compare variants in DNA and RNA
- Identify Candidate Variants and Genes from Tumor Normal Pair
- Identify variants and add expression values
- Identify and Annotate Differentially Expressed Genes and Pathways
Genome browser
- Track types
  - Visualizing, zooming and navigating tracks
- Create new genome browser view
- Genome browser view tools
- Graphs
Quality control tools
- QC for Target Sequencing
- QC for Sequencing Reads
- QC for Read Mapping
  - Running the 'QC for Read Mapping' tool
Preparing raw data tools
- Merge overlapping pairs
  - Using quality scores when merging
  - Report of merged pairs
- Trim Reads
- Demultiplex reads
  - An example using Illumina barcoded sequences
Resequencing analysis tools
- Map Reads to Reference
  - Selecting reads and reference
  - Including or excluding regions (masking)
  - Mapping parameters
  - Mapping paired reads
  - Non-specific matches
  - Gap placement
  - Mapping computational requirements
  - Reference caching
- Mapping output
  - Mapping output options
  - Mapped reads coloring
  - Reads track output from a read mapping
- Summary 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 reads based on overlap
- 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
- Copy Number Variant Detection
  - Running 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
- Coverage analysis
- 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
- Identify Known Mutations from Sample Mappings
  - How to run the Identify Known Mutations from Sample Mappings tool
  - Output from the Identify Known Mutations from Sample Mappings tool
Add information to variants tools
- Add information from variant databases
- Add conservation scores
- Add exon number
- Add flanking sequence
- Add fold changes
- Add information about amino acid changes
- Add information from genomic regions
- Add information from overlapping genes
- Link Variants to 3D Protein Structure
  - Method details
- Download 3D Protein Structure Database
- From databases
Remove variants tools
- Remove variants found in external database
- Remove variants not found in external database
- Remove false positives
- Remove Germline Variants
- Remove reference variants
- Remove variants inside genome regions
- Remove variants outside genome regions
- Remove variants outside targeted regions
- From databases
Add information to genes tool
- Add information from overlapping variants
Compare samples tools
- Compare shared variants within a group of samples
- Identify Enriched Variants in Case vs Control Group
- Trio analysis
Identify candidate variants tools
- Identify candidate variants
- Remove information from variants
- Identify variants with effect on splicing
Identify candidate genes tools
- Identify differentially expressed gene groups and pathways
- Identify highly mutated gene groups and pathways
- Identify mutated genes
- Select genes by name
RNA-Seq Analysis tools
- RNA-Seq analysis
- Create Combined RNA-Seq Report
- Create fold change track
- PCA for RNA-Seq
  - Principal component analysis plot (2D)
  - Principal component analysis plot (3D)
- Differential Expression for RNA-Seq
- Create Heat Map for RNA-Seq
  - Clustering of features and samples
  - The heat map view
- Create Expression Browser
  - The expression browser
- Create Venn Diagram for RNA-Seq
  - Venn diagram table view
- Gene Set Test
Microarray and Small RNA Analysis tools
- Small RNA analysis
- 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
Helper tools
- Extract sequences
- Filter Based on Overlap
Cutting and cloning
- Restriction site analyses
  - Dynamic restriction sites
  - Restriction Site Analysis
- Restriction enzyme lists
- Molecular cloning
- Gateway cloning
- Gel electrophoresis
  - Gel view
Sequencing Data Analysis
- 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
- 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
Epigenomics
- ChIP-Seq Analysis
- Annotate with nearby gene information
Legacy tools
- Import Roche 454
- Import SOLiD
Appendix
- Use of multi-core computers
- Reference data overview
- 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
- Matrices for alignment calculation
Bibliography

Calculating expression values from RNA-Seq

When the reference has been defined, click Next and you are presented with the dialog shown in figure 29.10.

Image mrna_seq_step3
Figure 29.10: Defining how expression values should be calculated.

These parameters determine the way expression values are counted.

Subsections