Troubleshooting Files for Array Scans

Key File	Subfolder	Description
Scan parameters file (ScanParameters.xml)	<Run folder name>	Contains information about scan parameters. Information includes scan date, BeadChip barcode, cluster file location, and manifest file location.
Log files Log files	Logs	Log files describe each step performed on the instrument during the scan.
Metrics files Log files	[Barcode]	Metrics are provided as sample metrics and as section metrics. [barcode]_sample_metrics.csv—For each sample and channel (red and green), lists Percent Off Image, Percent Outliers, P05, P50, P95, Avg FWHM Avg, FWHM Stddev, and Min Registration Score. [barcode]_section_metrics.csv—For each section and tile, lists Laser Z-position, Through Focus Z-position, Red FWHM, Green FWHM, Red Avg Pixel Intensity, Green Avg Pixel Intensity, Red Registration Score, and Green Registration Score.
Rescan file Log files	[Barcode]	[barcode]_rescan.flowcell—Lists the tile locations adjusted for a rescan, which include an increased tile-to-tile overlap.

Scan parameters file

(ScanParameters.xml)

Contains information about scan parameters. Information includes scan date, BeadChip barcode, cluster file location, and manifest file location.

Log files
Log files

Logs

Log files describe each step performed on the instrument during the scan.

Metrics files
Log files

[Barcode]

Metrics are provided as sample metrics and as section metrics.

[barcode]_sample_metrics.csv—For each sample and channel (red and green), lists Percent Off Image, Percent Outliers, P05, P50, P95, Avg FWHM Avg, FWHM Stddev, and Min Registration Score.

[barcode]_section_metrics.csv—For each section and tile, lists Laser Z-position, Through Focus Z-position, Red FWHM, Green FWHM, Red Avg Pixel Intensity, Green Avg Pixel Intensity, Red Registration Score, and Green Registration Score.

Rescan file
Log files

[Barcode]

[barcode]_rescan.flowcell—Lists the tile locations adjusted for a rescan, which include an increased tile-to-tile overlap.