Appendix C Output Files and Folders
Sequencing Output Files 59
Sequencing Output Folder Structure 61
Scanning Output Files 62
Scanning Output Folder Structure 63
Sequencing Output Files
File Type File Description, Location, and Name
Base call files Each tile analyzed is included in a base call file, aggregated in 1 file for each lane, for each
cycle. The aggregated file contains the base call and encoded quality score for every cluster for
that lane.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
[Cycle].bcl.bgzf, where [Cycle] represents the cycle number in 4 digits. Base call files are
compressed using block gzip compression.
Base call index file For each lane, a binary index file lists the original tile information in a pair of values for each
tile, which are tile number and number of clusters for the tile.
Base call index files are created the first time a base call file is created for that lane.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
s_[Lane].bci
Cluster location files For each tile, the XY coordinates for every cluster are aggregated into 1 cluster location file for
each lane. Cluster location files are the result of template generation.
Data\Intensities\L00[X]—Files are stored in 1 folder for each lane.
s_[lane].locs
Filter files The filter file specifies whether a cluster passed filters. Filter information is aggregated into 1
filter file for each lane and read.
Filter files are generated at cycle 26 using 25 cycles of data.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
s_[lane].filter
InterOp files Binary reporting files used for Sequencing Analysis Viewer (SAV). InterOp files are updated
throughout the run.
InterOp folder
RTA configuration
file
Created at the beginning of the run, the RTA configuration file lists settings for the run.
[Root folder], RTAConfiguration.xml
Run information file Lists the run name, number of cycles in each read, whether the read is an indexed read, and
the number of swaths and tiles on the flow cell. The run info file is created at the beginning of
the run.
[Root folder], RunInfo.xml
Flow Cell Tiles
Tiles are small imaging areas on the flow cell defined as the field of view by the camera. The total
number of tiles depends on the number of lanes, swaths, and surfaces that are imaged on the flow cell,
and how the cameras work together to collect the images.High-output flow cells have a total of 864
tiles.
Document # 1000000041922 v01
For Research Use Only. Not for use in diagnostic procedures.
59
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