73e5ffe87841338f4519f9a88558d9d7e7aa6bc8 kuhn Wed Feb 12 12:33:24 2020 -0800 expanded descripiton of doWiggle a little diff --git src/hg/htdocs/goldenPath/help/bam.html src/hg/htdocs/goldenPath/help/bam.html index b4c6cc6..1d86685 100755 --- src/hg/htdocs/goldenPath/help/bam.html +++ src/hg/htdocs/goldenPath/help/bam.html @@ -105,31 +105,31 @@ <strong>bamGrayMode </strong><em>aliQual|baseQual|unpaired </em> # grayscale metric, default is aliQual <strong>bamColorTag </strong><em>XX </em> # optional tag for RGB color, default is "YC" <strong>minAliQual </strong><em>N </em> # display only items with alignment quality at least N, default 0 <strong>showNames </strong><em>on|off </em> # if off, don't display query names, default is on </code></pre> Other optional settings are not specific to BAM, but relevant: <pre><code> <strong>name </strong><em>track label </em> # default is "User Track" <strong>description </strong><em>center label </em> # default is "User Supplied Track" <strong>visibility </strong><em>squish|pack|full|dense|hide</em> # default is hide (will also take numeric values 4|3|2|1|0) <strong>priority </strong><em>N </em> # default is 100 <strong>db </strong><em>genome database </em> # e.g. hg18 for Human Mar. 2006 <strong>maxWindowToDraw </strong><em>N </em> # don't display track when viewing more than N bases <strong>chromosomes </strong><em>chr1,chr2,... </em> # track contains data only on listed reference assembly sequences - <strong>doWiggle </strong><em>on|off </em> # if on, show density graph, default is off + <strong>doWiggle </strong><em>on|off </em> # if on, show data as density graph, default is off </code></pre> <p> The <a href="hgBamTrackHelp.html" target="_blank">BAM track configuration</a> help page describes the BAM track configuration page options corresponding to <code>pairEndsByName</code>, <code>minAliQual</code>, <code>bamColorMode</code>, <code>bamGrayMode</code> and <code>bamColorTag</code> in more detail.</p> <p> <code>pairSearchRange</code> applies only when <code>pairEndsByName</code> is given. It allows for a tradeoff of display speed vs. completeness of pairing the paired-end alignments. When paired ends are split or separated by large gaps or introns, but one is viewing a small genomic region, it is necessary to search a large number of bases upstream and downstream of the viewed region in order to find mates of the alignments in the viewed region. However, searching a very large region can be slow, especially when the alignments have deep coverage of the genome. To ensure that all properly paired mates will be found, <code>pairSearchRange</code> should be set to the largest genomic size