illumina HiSeq X, User Manual, Page: 70 / 86

R
e
a
l-
T
im
e
A
n
a
lysi
s
60
Part # 15050091 Rev. C
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 —One file for the run is stored in the Intensities folder.
s.locs
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
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