BlueFuse Multi Software FAQs

The following Illumina products are compatible with analysis in the CytoChip and Karyomapping BlueFuse Multi Modules:

CytoChip Module

• Infinium CytoSNP-850K
• Infinium CytoSNP-12
• Veriseq PGS

Karyomapping Module

• Infinium Karyomap-12

To install and register BlueFuse Multi, download the software from Product Files. 

Once you have downloaded and installed the software, send the registration file request to techsupport@illumina.com to receive a registration file to register the software.

To get your registration codes, select Help | About, and then click Registration on the About dialog.

Upgrade BlueFuse Multi by running the latest BlueFuse Multi version installer.

After you have upgraded the BlueFuse Multi Software, you will be prompted to upgrade an existing database the first time you access it. Go through the prompts of typing ‘123’ and click "OK" to upgrade the existing database. 

1. Select views in the side panel.
2. Click and drag the boundaries and title bars of the views to configure the sizes and locations on the screen.
3. Click Tools | Manage Shortcuts.
4. Enter a name for your custom view and click Add Current.
5. You can also reorder the list or remove any shortcuts.
6. Click OK to save the new settings to the database.

Only administrators and supervisors can set a custom report configuration.

1. Click Tools | Global Configuration | Custom Report Configuration.
2. Select Experiment Type.
3. Select the information required in the report. For more information, see the "Report Contents" section in the BlueFuse Multi Software Guide.
4. Click Save All or Save Current to save the new settings to the database.

A database stores the information required to run the software and saves the data generated from BlueFuse Multi analysis. Create the database on the local computer drive or on a networked drive.

Classic Mode:

1. Click Tools | Change Database Path.
2. Browse to the directory for the new database. Use the full UNC path that is used for locating databases to improve speeds across the network.
3. Click Make New Folder, and then name the new database.
4. Fill in the administrator details.
5. Click OK.
6. Import an annotation database

Server Mode:

1. Click Tools | Change Database Path.
2. Select Connect to Database Server.
3. Enter the Host directory path for the server.
4. Enter the Port directory. The default is 12345.
5. Browse to the directory for the new database.
6. Click Make New Folder, and then name the new database.
7. Fill in the administrator details.
8. Click OK.
9. Import an annotation database.

Download the annotation database from Product Files.

To import an annotation database into a BlueFuse Multi database:

1. In BlueFuse Multi, go to Tools | Import New Annotation
2. Browse to the downloaded, extracted annotation database file and click Open. 

In BlueFuse Multi, go to Tools | Change Database Path, and select the top-level directory for the database folder.

If the database is from an older version of BlueFuse Multi, the software will prompt to perform a database upgrade. Follow the prompts and click "OK" to upgrade the database.  

BlueFuse Multi software does not specify a maximum database size. The limitation will be the capacity of the drive that hosts the database folder. Please note that increased database size may result in slower performance due to hardware and network limitations. 

BlueFuse Multi manages a hidden set of folders/files and requires all of them to be present. You may only copy/move the entire database hierarchy along with ALL of the files/subfolders within it. If you delete any individual files or hidden folders BlueFuse Multi may cease to function. In general, and certainly before moving the entire database, we would recommend you first obtain a full back-up.

1. Select the top-level database folder.
2. Right-click, and then click Copy.
3. Paste the folder in the destination location

If other users are currently using the database, do not copy or move it. Large databases can take a long time to copy. It is recommended to perform the process overnight.

For VeriSeq PGS, store the original sequencing run folder in a different folder from the database to have a record of all raw data. If necessary, this data can be used to reimport data into BlueFuse Multi.

1. Click Users | Reset Admin Password.
2. A new, random password is generated. Click Copy to Clipboard, and email the password to techsupport@illumina.com. 
3. Illumina support will return an email with a text string. Enter the text string in the verification box.
4. Click OK to set the new password.
5. To change this password after the reset, go to Users | Change Password.

BlueFuse Server has not been validated on a virtual environment by Illumina. Please see the supported operating systems and hardware requirements on Computing Requirements. Using a virtual machine may negatively impact performance of BlueFuse Server.

1. Open BlueFuse Multi Cytochip Module and log in.
   
2. Under File menu, select Batch | Batch Import.
   
3. Navigate to the Samplesheet.txt or Samplesheet.csv file in the run folder, select, and click Open.
   
4. In the following dialog box, select the appropriate annotation database file in the dropdown menu.
5. Check the box next to "Start processing images automatically after import."
6. Click Import. 

Information about calling of mosaic samples or segmental changes in BlueFuse Multi can be found in the Mosaic Samples section of the VeriSeq PGS Technical Guide to Aneuploidy Calling.

Information about interpreting VeriSeq PGS results in BlueFuse Multi can be found in the VeriSeq PGS Technical Guide to Aneuploidy Calling.

Guidelines for recommended QC measures for VeriSeq PGS runs can be found in the VeriSeq PGS-MiSeq QC Assessment Guide.

Each sample is independently compared against the in silico reference dataset—because of this, it does not matter how many and what aberrations are in the sample set for a single run.

A Batch Import file can be created using the CytoSNP-850K Lab Planner tool. Once the batch import .txt file has been generated, go to File|Batch|Batch Import, locate the batch import file, then click Open.

More information can be found in the Import 24sure and BeadArray Experiments section of the BlueFuse Multi Software Guide.

BlueFuse Algorithm settings can be modified by going to Tools | Array Configuration | Array Algorithm settings.

For more information on the customizable algorithm settings, see the Array Algorithm Settings section of the BlueFuse Multi Software Guide.

FFPE samples can be run on CytoSNP-850K with the Infinium FFPE QC Kit and the Infinium FFPE Restore Kit. 

FFPE-specific manifest and cluster files can be downloaded on the CytoSNP-850K support page. 

A mask file can be created in the standard BED file format to exclude genomic regions from region calling and visualization. For more information about genome masking in BlueFuse Multi, see the Genome Masking section in the BlueFuse Multi Software Guide.

To analyze data with a different cluster file in BlueFuse Multi, the .gtc files will have to be regenerated from the raw .idat scan files. This can be performed with the Beeline Software. 

An orange SNP dot in the B Allele Frequency plot indicates that the genotype is a "No Call" due to not being called as AA, AB, or BB during genotype analysis. A SNP designated NC does not mean the data point is not informative for the analysis, as these SNPs are included in the calling algorithm. 

Introduced in BlueFuse Multi v4.4, new views are available that allow users to perform Duo and Trio genotype analysis using Illumina BeadChip experiments. Detailed information can be found in the Genotype Analysis section in the BlueFuse Multi Software Guide.