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Monitor Run Metrics

HiSeq 2500 System User Guide

115

Monitor Run Metrics

Real-TimeAnalysis automatically generates quality metrics when image analysis begins.

However, not all metrics are available at the early cycles because some processes need

multiple cycles to generate data.

Data Cycle

Image analysis After cycle 5.

During the first 5 cycles of the run, the software generates a

template of cluster locations.

Base calls After cycle 12.

Base calling begins after the color matrix is estimated at cycle 12.

Phasing estimates After cycle 25.

The phasing corrections for the first 25 cycles determine the

phasing estimate.

Quality scores After cycle 25.

A quality score is generated for reads that pass the quality filter.

Because quality scores require corrected intensities from future

cycles, quality scoring always follows base calling.

Error rates After cycle 25.

Error rates are generated only when PhiX clusters are present

and the Align to PhiX option is selected during run setup.

In-line controls At cycle 52 of each read, or at the end of the run for runs with

fewer than 52 cycles.

In-line controls are generated only for TruSeq library preparation

methods.*

Index count After the index reads are complete.

The index count per lane is generated only when a sample sheet

is provided.

*Sequencing Analysis Viewer v1.8.44 and later no longer includes the TruSeq Controls tab, where

SAVreports the results of the analysis of the in-line controls.

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Directed Electronics equalizer 2500 Betriebsanweisung Seite 125