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This section of the Affymetrix Learning Center provides training on Affymetrix Genotyping Console 2.1, an improved software package for genotyping, copy number and loss of heterozygosity (LOH) analysis. This software enables workflows for single or large numbers of samples, and includes the Genotyping Console Browser for viewing results in chromosomal and whole-genome contexts.

Part 1: Introduction and installation

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• CN/LOH analysis workflow overview
• Downloading and installation process
• User profiles and library path
• Workspaces, data sets, adding data
• QC checks and automation

Part 2: Single or multi-sample CN/LOH workflow

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• Toolbar icons and functionality
• CN/LOH overview
• Create data set, check contrast QC, run CN/LOH algorithm
• Segment Reporting Tool
• Custom regions
• Copy number segment report
• Custom regions report

Part 3: Genotyping Console Browser

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• Choosing CNCHP and CN_SEGMENTS files
• Karyoview
• Segment Report
• Single chromosome view
• Searching browser annotation
• External database links
• Graph properties
• Graph types: LOH, allele difference, smooth signal (for Mosaicism)
• Gender calls
• CN-neutral LOH
• Allele difference graph and long, contiguous stretches of homozygosity

Part 4: Other features and advanced workflows

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• BED files of all SNP Array 6.0 markers
• CN_INPUT_REGIONS in browser
• Configurations: CN/LOH config editing/creation advanced options
• Reference model file creation
• Miscellaneous
• Show locations in workspace dialog full file paths
• Edit sample file pre-existing fields
• Genotype concordance checks

Related Content

Whole-genome Association Studies
Genotyping Console™ Software

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