Generate an Illumina Marker Map

Open your project BeadStudio project.

To generate the marker map Select >Analysis >Reports >Report Wizard.

Figure 1. BeadStudio interface.

On the window that pops up, check Final Report and click Next (Figure 2).

Figure 2. Genotyping Report window.

Select the samples you want and click Next again (Figure 3).

Figure 3. Selecting samples in the Genotyping Report window.

On the Final Report Format window (Figure 4), Check the box under the General Options section labeled Create map files. Click Next.

Figure 4. Final Report Format window.

Select the location to save the map files and click Finish.

BeadStudio will then proceed to output three files - two map files and a comma delimited text file containing all alleles for all genotypes. If you don’t want to wait for the allele text file, which could take a very long time, click Cancel once the first sample (or SNP depending on the options chosen in the previous step) has started. The map files are created first and will be saved to the location you specified.