Can GenomeStudio 2.0 genotyping projects be merged?

GenomeStudio 2.0 *.bsc files are standalone projects and cannot be merged. However, i****t is possible to combine multiple data sets.

If the data was generated using the same beadchip type and version:

Option 1: Re-create a new GenomeStudio 2.0 project combining all samples into one large project

Option 2: Load additional samples to existing project. In GenomeStudio 2.0, select File > Load Additional Samples. The user can specify a sample sheet or directories to load intensity files.

Considerations:

• User will need access to raw data (idats or gtcs).

• A large number of samples can cause the software to slow down or crash.

• Each beadchip type/version has its own unique manifest. Data from different beadchip types/versions cannot be combined into one project.

• Only one manifest can be used for a GenomeStudio project. Previously, multiple manifests could be used to load a GenomeStudio genotyping project. However, this is no longer possible with the latest version of GenomeStudio.

• If using a sample sheet to load additional samples, only the new samples need to be included in the sample sheet. There is no need to upload a sample sheet that combines both existing and additional samples.

Note: After importing additional data, a filter may automatically be applied. There may be hidden rows in the Samples Table and only a subset of samples may be visible. The displayed subset of samples could either be the old samples only, or the newly added samples only.

The bottom of the Samples Table shows the total number of samples in the project ("Rows") and the displayed rows ("Disp").

To view all the samples in the project, select the "Clear filter" button. All the sample rows should now be visible.

If the data comes from 2 or more different beadchip types and/or versions:

1. Create a separate GenomeStudio 2.0 project with appropriate manifest and cluster file for each beadchip type.

2. Generate a Final Report for each project selecting desired parameters.

3. Merge data in Microsoft Excel or other software.

For any feedback or questions regarding this article (Illumina Knowledge Article #3847), contact Illumina Technical Support [email protected].