6.8 years ago by
EMBL Heidelberg / de.NBI
So Illumina tech support got back to me with the following instructions for obtaining bead-level data. I don't have access to an iScan machine, so if anyone could reply with whether it was successful or not, that would be great.
Thank you for your request. Luckily, collecting bead level data on an iScan is much easier than on a BeadArray reader.
-After launching the iScan Control Software, go to the Menu Arrow at the top left and Options.
-Select Scan settings, go to the scan settings file for your beadChip product and create a copy using the Copy button at the bottom of the window (Note: original scan setting files cannot be modified!).
-Name the new Scan Settings (.scst) file with a name reflecting that it is collecting
Bead level data (e.g. InfiniumHDbeadlevel.scst) and save.
-Click on the new file you created under Scan settings. Under Analysis make sure that ‘Include Outliers’ is set to ‘true’ if you want to collect data from every bead, or ‘false’ if you would not like to collect outlier beads.
-In the Output section, you will define whether or not you wish to ‘Export Bead
Data’ which means exporting a text file with intensity values for each individual bead. In
this case, we want to set this to ‘true’. Export Bead Type data = True will give a text file indicating the average bead intensity for each Bead Type. You can also define whether or not to ‘Include XY in Bead Data’. This will indicate whether X, Y pixel coordinates will be saved in the Bead Data file if Export BeadData is set to ‘true’. Set this option to ‘true’.
Before starting the scan, please make sure to point to the new scan settings, not the default scan settings file.