Output Files

Images are passed in memory to RTA2 as tiles, which are small imaging areas on the flow cell defined by one camera view. The iSeq 100 iSeq 100 i1 Flow Cell Flow Cell has 16 tiles.

From these images, RTA2 produces a set of quality-scored base call files and filter files as primary output. Other files support generation of the primary output.

File Type

File Description, Location, and Name

Base call files

Each tile analyzed is included in a base call file, aggregated in one file per cycle. The aggregated file contains the base call and associated quality score for every cluster.

Data\Intensities\BaseCalls\L001

[Cycle].bcl.bgzf, where [Cycle] represents the cycle number in four digits. Base call files are compressed using block gzip compression.

Base call index files

A base call index file preserves the original tile information. For each tile, the index file contains the tile number and number of clusters.

Data\Intensities\BaseCalls\L001

s_1.bci

Cluster locations file

One cluster location (s.locs) file contains the X,Y coordinates for every cluster on the flow cell.

Data\Intensities

s.locs

Filter files

Filter files specify whether clusters pass filter. For each tile, one filter file is generated. Filter files are generated at cycle 26 using 25 cycles of data.

Data\Intensities\BaseCalls\L001

s_[lane].filter

InterOp files

Real-time metrics of run quality that are updated throughout the run. These binary files contain tile, cycle, and read-level metrics, and are needed to view metrics in Sequencing Analysis Viewer.

InterOp folder

RTA configuration file

Lists parameters for the run. Created at the beginning of the run, the file combines values from the input configuration file and values that RTA2 defines.

[Root folder], RTAConfiguration.xml

Run information file*

Lists the run name, number of cycles per read, whether the read is an Index Read, and the number of swaths and tiles. Created at the beginning of the run.

[Root folder], RunInfo.xml

Thumbnail files

Thumbnail images of flow cell tiles.

Images\L001\C[X.1]—Files are stored in one folder for each lane and one subfolder for each cycle.

s_[lane]_[tile].jpg—The thumbnail image includes the tile number.

*Created by the control software. RTA2 creates all other files listed in the table.

Local Run Manager and BaseSpace Sequence Hub automatically convert base calls files into FASTQ files. When sequencing in Manual mode, use the latest version of the bcl2fastq2 Conversion Software to convert FASTQ files. Download the software from the bcl2fastq Conversion Software support pages on the Illumina website.

For each run, the control software automatically generates an output folder and a run folder. Access the run data from the output folder, which is a copy of the run folder. The run folder is for system use.

The path to the output folder is user-defined, but defaults to D:\. The control software names the output folder using the following format.

Format

Example

<YYYYMMDD>_<Instrument ID>_<Run Number>_<Flow Cell ID>

20180331_FFSP247_4_BNS417-05-25-12

The run number increments by one each time the system performs a run. Serial numbers identify the instrument and flow cell.

Recipe—Run-specific recipe file.

Logs—Log files describing instrument analytics, operational steps, and other events.

Config—Configuration settings for the run.

RunParameters.xml

RunInfo.xml

CopyComplete.txt

RunCompletionStatus.txt

RTAComplete.txt

RTAConfiguration.xml

Data

Intensities

BaseCalls

L001

s.locs

InterOp

Images

SampleSheet.csv—Sample sheet or the sample manifest.

RTALogs—Log files describing RTA2 events.