Ctrlk
Illumina Connected SoftwareIllumina.comIllumina Support
For the complete documentation index, see llms.txt. This page is also available as Markdown.

Using Beeline to regenerate GTC files with an alternate cluster file or manifest file

GTC files are generated from IDAT files using the AutoConvert feature within the iScan Control Software (ICS) or NextSeq 550 Control Software (NCS). Occasionally, users will want to generate alternate GTC files applying a custom or updated cluster file, or an updated manifest file that is different from the ones used to create the original GTC files. Such GTC files can be regenerated using existing IDAT files and the Beeline 2.0 software.

  1. Download the Beeline software v.2.0.3 from the Beeline Support page.

  2. Upon launching the Beeline software, a welcome screen appears with the application windows . Select “Close” in the bottom right corner.

Figure 1. Beeline welcome screen

  1. In the next screen, select the "Convert Idat to Gtc" icon.

.

Figure 2. Convert Idat to Gtc menu

  1. Follow the instructions on page 11 of the Beeline Software User Guide and browse to the IDAT Folder, Manifest file, and Cluster File.

.

Figure 3. IDATs, Manifest and Cluster File selection screen

Notes:

  • Beeline is expecting the IDAT files to be contained in a folder that has the same name as the barcode of the IDATs, eg, 203561980081. In Beeline, one can designate the IDATs folder either as the direct barcode folder, or the folder containing the barcode folder, one level up.

  • For Beeline to work, the IDATs need to have the original name. If the IDATs have been renamed, edit back to the original name, eg, "203561980081_R02C01_Red.idat."

  • If renaming the cluster file, be aware that the custom cluster file name must match the Illumina convention up to the first “underscore”, eg, CytoSNP-850Kv1-2_custom-text-here.egt

  • If working in GenomeStudio v2.0, one can create a new project using the new GTC files and a sample sheet (required). Regenerate the CN Metrics report and check the LogRDev values in GenomeStudio v2.0 as usual.

For any feedback or questions regarding this article (Illumina Knowledge Article #2205), contact Illumina Technical Support techsupport@illumina.com.

Last updated

Was this helpful?