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Real-Time Analysis Overview

HiSeq 2500 System User Guide

113

Real-Time Analysis Overview

Real-Time Analysis runs on the instrument computer, performing base calling and

assigning a quality score to each base call.

The software tracks the status of each tile and determines when to advance it to the next

process step. When advancing a tile, Real-Time Analysis outputs a file for the completed

step and then starts the next step. Thus, the software can determine the status of each tile

based on which files exist. If Real-Time Analysis is terminated, it saves run data and can

resume processing.

Real-Time Analysis Input

Real-Time Analysis requires the following input files:

} Cluster intensity files, which contain image analysis results.

} RunInfo.xml, which the control software generates automatically at the beginning of the

run. From this file, Real-Time Analysis reads the run name, number of cycles, whether

a read is indexed, and the number of tiles on the flow cell.

} HiSeq.Configuration.xml, which is an instrument configuration file in XML format.

} RTA.exe.config, which is a software configuration file in XML format.

Real-Time Analysis uses run parameters entered during run setup, and receives commands

from the control software that include information about when to initiate and the location

of RunInfo.xml.

Real-Time Analysis Output

Tiles are small imaging areas on the flow cell defined as 1 field of view by the camera. For

each tile that is analyzed, Real-Time Analysis produces a set of quality-scored base call

files and filter files as primary output. 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 (*.locs) file contains the X,Y coordinates for

every cluster on the flow cell.

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Directed Electronics equalizer 2500 Betriebsanweisung Seite 123