Generate Normalized Data and Genotype Calls
A BeadChip scan generates intensity data (*.idat) files. These files contain raw intensity data values for every bead on the scanned image. For more information on IDAT files, refer to Generated Files.
You can configure iScan Control Software to normalize the data in these files. Normalization transforms the range of intensity values for a BeadChip stripe to match a target range, resulting in faster downstream processing times and optimized workflow. Normalized data and associated genotype calls are saved in genotype call (*.gtc) files.
iCS includes an automated genotype calling feature, called AutoConvert. AutoConvert automatically converts IDAT files to GTC files during scanning, on a per-chip basis, for use in downstream analysis software such as Beeline or GenomeStudio Software.
Configuring iCS to normalize your data requires you to set up a mapping file that associates a type of BeadChip with its manifest and cluster files.
You cannot use AutoConvert if using Laboratory Information Management System (LIMS). LIMS uses its own built-in automated genotype calling feature, called AutoCall. For more information on LIMS AutoCall, refer to the Illumina LIMS User Guide and the Illumina LIMS Project Manager Guide.
Enable AutoConvert and Generate Normalized Data
To generate normalized data for faster downstream processing times and optimized workflow, complete the following steps:
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1.
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From the menu in the upper left corner of the screen, select Tools, and then select Options. |
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2.
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In the Options dialog box, select the AutoConvert tab. |
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3.
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Select the Enable AutoConvert checkbox. |
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4.
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Browse to an existing mapping file, or select New to create a mapping file now. |
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5.
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[Optional] Edit the mapping file as follows: |
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a.
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Select Edit Mapping File. |
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b.
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In the AutoConvert Mapping dialog box, highlight the mapping you want to edit or select New to create a mapping. For a new mapping, the row is populated with default entries. |
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c.
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Select the PartNumber field in the right pane and enter or edit the product part number of the BeadChip. The product part number can be found on the BeadChip packaging. |
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d.
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Select the ManifestFilePath field, select the browse control, and then navigate to and select the bead pool manifest file (*.bpm). |
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e.
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Select the ClusterFilePath field, select the browse control, and then navigate to and select the bead cluster file (*.egt). |
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6.
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In the Options dialog box, select OK. |
