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HiSeq X System User Guide
55
Real-Time Analysis Workflow
The Real-Time Analysis workflow includes the following steps:
}
Template generation
—Maps cluster locations.
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Registration and intensity extraction
—Records the location of each image on the
patterned flow cell and determines an intensity value for each cluster.
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Color matrix correction
—Corrects cross talk between channels.
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Empirical phasing correction
—Corrects the effects of phasing and prephasing.
}
Base calling
—Determines a base call for every cluster.
}
Quality scoring
—Assigns a quality score to every base call.
Template Generation
The first step of the workflow is template generation, which defines the position of each
cluster in a tile using X and Y coordinates. The template is used as a reference for the
subsequent step of registration and intensity extraction.
Because of the array on the patterned flow cell, cluster positions are predetermined
according to the number of rows, number of columns, and distance between the nano-wells
on the flow cell. For more information, see
.
Cluster positions are written to 1 cluster location (s.locs) file for the entire run. For more
information, see
Registration and Intensity Extraction
Registration and intensity extraction begin after the template of cluster positions is
generated.
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Registration transforms the template locations of clusters to the location on the image
in each of the 4 color channels.
}
Intensity extraction determines an intensity value for each cluster in the template for a
given image.
If registration fails for any images in a cycle, no base calls are generated for that tile in that
cycle. Use the Sequencing Analysis Viewer to examine thumbnail images and identify
images that failed registration. Use the offsets files for troubleshooting registration issues.
For more information, see