The Affymetrix® Chromosome Analysis Suite (ChAS) was developed with input from leading researchers, so it's specifically targeted to cytogenetic analysis and reporting. Features, including a streamlined analysis workflow, multiple graphical views, and flexible analysis options, are presented in an easy-to-understand graphical interface. With this unique software, you can analyze data and generate reports based on your specific requirements.
Related Content
This section of the Online Training provides step-by-step instructions for analyzing a sample. Watch the videos below to learn how you can view results in chromosomal and whole-genome contexts with the integrated browser and use our simple drop-down menus and visualization tools to access your data quickly, perform quality checks, and explore biological relevance.
Installation: ChAS Software and CytoScan™ HD analysis files (13:00)
This section outlines the required system specifications, along with the appropriate files to download and install. It also includes a demo of the installation.
Launching ChAS and running a single sample analysis (8:00)
This section describes how to launch ChAS, set it up to start processing data, and then process and view your final data.
ChAS browser overview and introduction to copy number segment data (16:00)
This section guides you through opening a CYCHP file and gives you an overview of the ChAS browser. You will also learn about browser settings, quality control (QC) and gender information, the difference between a gain and a loss, what smoothing and joining is, and how to read the segments table.
Copy number and SNP allele data types (21:00)
This section describes the use of the copy number and SNP allele data and how to visualize it.
Mosaicism (7:00)
This section describes how to use the smooth signal and allele peaks data in ChAS to determine if the sample you are viewing is mosaic.
Reference annotations (8:00)
This section describes the reference file annotations displayed from the ChAS Browser and the NetAffx Genomic Annotations files that are used in ChAS.
Creating your own annotation file for regions of interest (CytoRegions) (16:00)
This section describes how to make an AED file to track regions of special interest such as genes and disease regions, and then how to differentially filter Segments using that file (CytoRegions functionality).
Creating your own file to filter data out (Overlap Map) (4:00)
This section describes how to track regions of benign or artifact copy number, and then potentially filter segments out which would otherwise be found in those regions (OverlapMap functionality).
Reporting (11:00)
This section describes the various reporting options within ChAS.