Modifying sample sheet information and requeueing VeriSeq PGS analyses in MiSeq Reporter

10/20/17


Secondary analysis of VeriSeq PGS data on the MiSeq starts with the generation of BAM (alignment) files by MiSeq Reporter. These BAM files are then imported into the BlueFuse Multi software to perform the subsequent whole chromosomal aneuploidy calling. The import of BAM files into BlueFuse Multi can fail if there are errors or discrepancies in the sample sheet. Example cases where users might need to modify information contained in the sample sheet are:

  • A typographical error was introduced when entering the flow cell ID into the sample sheet. BlueFuse Multi will not import the BAM files if it detects a mismatch between the flow cell ID used in the sample sheet and the flow cell ID recorded by the RFID system within the raw data.
  • The embryo cycle or sample information was entered incorrectly. Correct the information in the sample sheet before processing or reprocessing in BlueFuse Multi.

To make changes to the sample sheet:

  1. On the MiSeq PC, go to D:\Illumina\MiSeq Analysis\ <run folder>. Create a backup copy of the SampleSheet.csv file.
  2. Edit the original SampleSheet.csv file in Notepad or Excel and make the required corrections.
  3. Save the edited sample sheet with the name SampleSheet.csv.
  4. Requeue the run for analysis in MiSeq Reporter. To requeue, open a web browser and navigate to http://localhost:8042 (the MiSeq Reporter interface). Select the Analyses button, check the Requeue box next to the run, and select the Requeue button.
  5. A new alignment folder, Alignment 2, is created in D:\Illumina\MiSeq Analysis\<run folder>\Data\Intensities\BaseCalls. The folder contains the new BAM files with the corrections from the new sample sheet incorporated.
  6. After analysis in MiSeq Reporter is complete, create a new analysis in the BlueFuse Multi Cytochip Module: select File > Batch > Batch Import.
  7. Navigate to the new alignment folder, Alignment 2, and select SampleSheetUsed.csv.
  8. Initiate the BlueFuse Multi analysis.