RTA Folders and Files

The following table describes the folders and files generated by Real-Time Analysis (RTA) during primary analysis. Many of these files are used for secondary analysis by the Local Run Manager software.

Key File

Subfolder

Description

RTAComplete.txt

Root folder

A marker file generated when base call analysis is complete. The presence of this file triggers the start of secondary analysis.

SampleSheet.csv

Root folder

This file is read and copied to the run folder before the run, and later used for secondary analysis.

RunInfo.xml

Root folder

Identifies the boundaries of the reads (including index reads) and the quality table selected for run.

*.bcl files

Data\
Intensities\BaseCalls\
L001\CX.X

Each *.bcl file contains RTA base calling and base quality scoring results for 1 cycle, 1 tile.

*.stats files

Data\
Intensities\BaseCalls\
L001\CX.X

*.stats files contain RTA base calling statistics for a given cycle/tile.

*.filter files

Data\
Intensities\BaseCalls

*.filter files contain filter results per tile.

*.txt

Data\RTALogs

Log files from primary analysis.

*.cif files

Data\
Intensities\L001\CX.X

Each binary *.cif file contains RTA image analysis results for 1 cycle, 1 tile. For more information, refer to Flow Cell Tile Numbering.

*.locs files

Data\
Intensities\BaseCalls\
L001

Reports the cluster coordinates. Each *.locs file represents 1 tile.

*.jpg files

Thumbnail_Images\
L001\CX.X

Thumbnail images generated for each cycle and base, and can be used to troubleshoot a run. These files are used for image analysis and are not copied to the Analysis folder. Refer to Flow Cell Tile Numbering for image file names.