r-bioc-shortread 1.36.0-1 / usr / lib / R / site-library / ShortRead / template / 3000-ReadDistribution.html

<h2>Read Distribution</h2>
<a name="Read-Distribution"></a>

<p>
  These curves show how coverage is distributed amongst
  reads. Ideally, the cumulative proportion of reads will transition
  sharply from low to high.
</p>
<p>
  Portions to the left of the transition might correspond roughly to
  sequencing or sample processing errors, and correspond to reads that
  are represented relatively infrequently. 10-15&#37;; of reads in a
  typical Genome Analyzer 'control' lane fall in this category.
</p>
<p>
  Portions to the right of the transition represent reads that are
  over-represented compared to expectation. These might include
  inadvertently sequenced primer or adapter sequences, sequencing or
  base calling artifacts (e.g., poly-A reads), or features of the
  sample DNA (highly repeated regions) not adequately removed during
  sample preparation. About 5&#37; of Genome Analyzer 'control' lane
  reads fall in this category.
</p>
<p>
  Broad transitions from low to high cumulative proportion of reads
  may reflect sequencing bias or (perhaps intentional) features of
  sample preparation resulting in non-uniform coverage. the transition
  is about 5 times as wide as expected from uniform sampling across
  the Genome Analyzer 'control' lane.
</p>
<pre>
  df &lt;- qa[["sequenceDistribution"]]
  ShortRead:::.plotReadOccurrences(df[df$type=="read",], cex=.5)
</pre>
@READ_OCCURRENCES_FIGURE@

<p>
  Common duplicate reads might provide clues to the source of
  over-represented sequences. Some of these reads are filtered by the
  alignment algorithms; other duplicate reads might point to sample
  preparation issues.
</p>
<pre>
  ShortRead:::.freqSequences(qa, "read")
</pre>
@FREQUENT_SEQUENCES_READ@

<p>
  Common duplicate reads after filtering
</p>
<pre>
  ShortRead:::.freqSequences(qa, "filtered")
</pre>
@FREQUENT_SEQUENCES_FILTERED@

<p>
  Common aligned duplicate reads are
</p>
<pre>
  ShortRead:::.freqSequences(qa, "aligned")
</pre>
@FREQUENT_SEQUENCES_ALIGNED@