Scanning Output Files - illumina NextSeq 550Dx Instrument Reference Manual

NextSeq 550Dx Research Mode Instrument Reference Guide
BaseCalls
L001—Base call files for lane 1, aggregated in 1 file per cycle.
L002—Base call files for lane 2, aggregated in 1 file per cycle.
L003—Base call files for lane 3, aggregated in 1 file per cycle.
L004—Base call files for lane 4, aggregated in 1 file per cycle.
L001—An aggregated *.locs file for lane 1.
L002—An aggregated *.locs file for lane 2.
L003—An aggregated *.locs file for lane 3.
L004—An aggregated *.locs file for lane 4.
Images
Focus
L001—Focus images for lane 1.
L002—Focus images for lane 2.
L003—Focus images for lane 3.
L004—Focus images for lane 4.
InterOp—Binary files used by Sequencing Analysis Viewer (SAV).
Logs—Log files describing operational steps.
Recipe—Run-specific recipe file named with reagent cartridge ID.
RTALogs—Log files describing analysis steps.
RTAConfiguration.txt
RunInfo.xml
RunNotes.xml
RunParameters.xml

Scanning Output Files

File Type
GTC files
Image files
Document # 1000000041922 v01
For Research Use Only. Not for use in diagnostic procedures.
File Description, Location, and Name
Genotype call file. A GTC file is generated for each sample scanned on the BeadChip.
The file name includes the barcode and sample scanned.
[barcode]_[sample].gtc
Image files are named according to the area scanned on the BeadChip. The name
includes the barcode, sample and section on the BeadChip, swath, and the imaging
channel (red or green).
[barcode]_[sample]_[section]_[swath]_[camera]_[tile]_[channel].jpg
• Barcode—The file name begins with the BeadChip barcode.
• Sample—An area of the BeadChip, which is numbered as a row (R0X), top to bottom,
and column (C0X) left to right.
• Section—A numbered row within a sample.
• Swath—BeadChips are imaged as a collection of overlapping tiles. Therefore, only 1
swath is used to image the section.
• Camera—The camera used to collect the image.
• Tile—An imaging area defined as the field of view by the camera.
• Channel—A channel is either red or green.
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