BlueFuse Multi important file types for analysis of BeadArray data using the CytoChip Module
BlueFuse Multi uses different file types during installation, experiment import, and data processing.
Infinium BeadArray data are generated from the iScan and NextSeq 550 system. See Illumina Knowledge article "Which Infinium beadchip types can be scanned using the NextSeq 550?" for additional information on compatible beadchips with the NextSeq 550.
The annotation database is required to analyze all array experiment types.
BlueFuse Multi General File Types
File Type
Description
File Extension
Brf
- BlueFuse Registration File obtained from Illumina Technical Support
- Required to register the copy of the software for versions 4.4 and below
.brf
GAL file (not used for BeadArray data)
- Issued for every array design, except for BeadArray.
- Contains information about the DNA and their locations on the microarray slide.
- Software extracts information from the scanned microarray image file and plots the position of the DNA probe on the genome against the fluorescent ratio value of the hybridized labeled DNA.
- After the GAL files are used in BlueFuse Multi, they are stored in the database.
.gal
Image File (not used for BeadArray data)
- For non-BeadArray arrays, scanned microarray images are saved in a TIFF (*.tif) file.
- All the scans (up to 2 prescans (Cy3 and Cy5) and 2 high-resolution scans) should be stored in a single file called a "multiframe" TIFF file.
- When naming the image file, include the barcode in the first or second string of the file name, and not buried within the name.
- From the barcode, BlueFuse Multi can automatically identify the type of array and assign the correct settings and files.
Note: The delimiter used in the file name can either be an underscore (_), dash (-), or space ( ).
.tiff
Annotation database
- Contains information about the human genome to aid in the interpretation of experimental results.
- Includes the position of genes, exons and publicly available data on CNV frequency shown in the DecisionTrack pane within BlueFuse Multi.
- Uses information from major public databases such as ENSEMBL for gene annotation, OMIM for inherited diseases, and DGV and dbVAR for genetic healthy or disease variants.
- Lists products eligible for analysis under the particular Annotation database. Products not listed cannot apply the Annotation database for analysis
- Used by BlueFuse Multi during analysis and visualization of experiments
.db
BeadArray-Specific File Types used with CytoChip Module
File Type
Description
File Extension
GTC
- Genotype call file that incorporates fluorescent image file information
- iScan software can be configured to create GTC file automatically as part of scanning or user may use Beeline software to convert IDATs to GTCs.
- BlueFuse Multi can automatically extract information from the GTC file name to identify the type of array, the barcode and specific subarray location on the slide, and assign the correct settings
.gtc
SNP Manifest File
- Contains SNP probe information
- Specific for each BeadArray design
- After the SNP manifest is used in a BlueFuse Multi database, it is stored in the database
.bpm
SNP Cluster File
- Provides reference information used in the analysis of the BeadArray
- After the SNP cluster file is used in a BlueFuse Multi database, it is stored in the database
.egt
Additional resources:
For any feedback or questions regarding this article (Illumina Knowledge Article #5043), contact Illumina Technical Support [email protected].
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