illumina HiSeq 2000, Системное руководство, Страница: 68 / 76

Appendix C Output Files and Folders
Sequencing Output Files 61
Output Folder Structure 62
Tile Numbering 62
Thumbnail Images 63
Sequencing Output Files
File Type File Description, Location, and Name
Base call files Each tile analyzed is included in a base call file that contains the base call and encoded
quality score.
Data\Intensities\BaseCalls\L00[X] —Files are stored in per cycle folders for each lane.
s_[Lane]_[Tile].bcl.gz , where lane is the single-digit lane number and tile is the 4-digit tile
number. Base call files are compressed using gzip compression.
Cluster location
files For each tile, 1 cluster location file contains the XY coordinates for every cluster. Cluster
location files are the result of template generation.
Data\Intensities
Filter files The filter file specifies whether a cluster passed filters. 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 and tile.
s_[lane]_[tile].filter
InterOp files Binary reporting files used for Sequencing Analysis Viewer. InterOp files are updated
throughout the run.
InterOp folder
Log files Record events and are updated throughout the run.
Data\RTALogs
Offsets files Two offsets files are created for each run:
• offsets.txt —Contains tile offsets for every cycle and channel relative to the template.
• SubTileOffsets.txt —Contains the measured shift for each quadrant of each image relative
to the frame of reference.
Data\Intensities\Offsets
Phasing files Contains empirical phasing information by tile. Phasing files are created at the first cycle
base called and updated after each cycle base called.
Data\Intensities\BaseCalls\Phasing
EmpiricalPhasing_[lane]_[read]_[tile].txt —Tile is represented with a 4-digit number that
indicates surface, swath, and tile.
Real-Time
Analysis
configuration file
Created at the beginning of the run, the Real-Time Analysis configuration file lists settings for
the run.
Data\Intensities
RTAConfiguration.xml
Statistics files Statistics created at base calling for each cycle.
Data\Intensities\Basecalls\L00[X]\C[X.1] —Files are stored in 1 folder for each lane and 1
subfolder for each cycle.
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
Thumbnail files A thumbnail image for each channel and tile in each swath at every cycle during imaging.
Thumbnail_Images\L00[X]\C[X.1] —Files are stored in 1 folder for each lane and 1 subfolder
for each cycle.
s_[lane]_[tile]_[channel].jpg —Tile is represented with a 4-digit number that indicates surface,
swath, and tile. See Tile Numbering on page 62 .
Document # 15011190 v03
For Research Use Only. Not for use in diagnostic procedures.
61