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HiSeq X System User Guide
53
RTA v2 Overview
RTA v2 runs on the instrument computer and extracts intensities from images, performs
base calling, and assigns a quality score to the base call.
Unlike previous versions of Real-Time Analysis software, RTA v2 and the control software
communicate through a web HTTP interface and shared memory files.
If RTA v2 is terminated, RTA v2 does not resume processing and run data are not saved.
Therefore, a run cannot resume after it has been stopped. RTA v2 resumes automatically
only if a run is paused.
RTA v2 Input
RTA v2 requires the following input files:
}
Tile images contained in local system memory.
}
RunInfo.xml, which the control software generates automatically at the beginning of the
run. From this file, RTA v2 reads the run name, number of cycles, whether a read is
indexed, and the number of tiles on the flow cell.
}
RTA.exe.config, which is a software configuration file in XML format.
RTA v2 receives commands from the control software that include information about the
location of RunInfo.xml file and if an optional output folder is specified.
RTA v2 Output
Images for each channel are passed in memory to RTA v2 as tiles. From these images, RTA
v2 produces primary output as a set of quality-scored base call files and filter files. Other
files support generation of primary output files.
}
Base call files
—For each tile that is analyzed, 1 compressed base call (*.bcl) file is
generated for each tile per cycle. The base call file contains the base call and associated
quality score.
}
Filter files
—Each tile produces filter information that is included in 1 filter (*.filter) file
for each tile over the whole run. The filter file specifies whether clusters pass filters.
}
Cluster location files
—One cluster location (s.locs) file contains the X,Y coordinates for
every cluster on the flow cell.
Primary output files are used for subsequent data analysis. Use the bcl2fastq v2.14
conversion software for demultiplexing and FASTQ conversion. To convert data from the