r-bioc-shortread 1.36.0-1 / usr / lib / R / site-library / ShortRead / template / 4000-CycleSpecific.html

<h2>Cycle-Specific Base Calls and Read Quality</h2>
<a name="Cycle-Specific-Base-Calls-and-Read-Quality"></a>

<p>
Per-cycle base call should usually be approximately uniform across
cycles. Genome Analyzer `control' lane results often show a deline in
A and increase in T as cycles progress. This is likely an artifact of
the underlying technology.
</p>
<pre>
  perCycle &lt;- qa[["perCycle"]]
  ShortRead:::.plotCycleBaseCall(perCycle$baseCall)
</pre>
@CYCLE_BASE_CALL_FIGURE@

<p>
Per-cycle quality score. Reported quality scores are `calibrated',
i.e., incorporating phred-like adjustments following sequence
alignment. These typically decline with cycle, in an accelerating
manner. Abrupt transitions in quality between cycles toward the end of
the read might result when only some of the cycles are used for
alignment: the cycles included in the alignment are calibrated more
effectively than the reads excluded from the alignment.
</p>
<p>
The reddish lines are quartiles (solid: median, dotted: 25, 75), the green line
is the mean. Shading is proporitional to number of reads.
</p>
<pre>
  perCycle &lt;- qa[["perCycle"]]
  ShortRead:::.plotCycleQuality(perCycle$quality)
</pre>
@CYCLE_QUALITY_FIGURE@