a10f1ce41547c142261ab3b3d71f8c487fa1f202 brianlee Sat May 7 08:12:23 2022 -0700 rephrasing sentence pointing to bigBed blog diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 1be93b2..93cd807 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -259,31 +259,31 @@ <a href="../goldenPath/help/customTrack.html#TRACK" target="_blank">track line</a>, and the name and position fields should uniquely describe items so that the correct ID and description will be displayed on the details pages.</p> <p> <strong><em>Example:</em></strong><br> This example uses the first 4 columns of BED format, but up to 12 may be used. Click <a class="insideLink" href="../cgi-bin/hgTracks?db=hg19&hgt.customText=http://genome.ucsc.edu/goldenPath/help/examples/bedDetailExample.txt" target="_blank">here</a> to view this track in the Genome Browser.</p> <pre><code>track name=HbVar type=bedDetail description="HbVar custom track" db=hg19 visibility=3 url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$" chr11	5246919	5246920	Hb_North_York	2619	Hemoglobin variant chr11	5255660	5255661	HBD c.1 G>A	2659	delta0 thalassemia chr11	5247945	5247946	Hb Sheffield	2672	Hemoglobin variant chr11	5255415	5255416	Hb A2-Lyon	2676	Hemoglobin variant chr11	5248234	5248235	Hb Aix-les-Bains	2677	Hemoglobin variant </code></pre> <p> -To see an example of turning a bedDetail custom track in a the <code>bigBed</code> +To see an example of turning a bedDetail custom track into the <code>bigBed</code> format, see this <a href="https://genome-blog.soe.ucsc.edu/blog/2021/08/03/how-make-a-bigbed-file-part-1/" target="_blank">How to make a bigBed file</a> blog post.</p> <a name="format2"></a> <h2>PSL format</h2> <p> PSL lines represent alignments, and are typically taken from files generated by BLAT or psLayout. See the <a href="../goldenPath/help/hgTracksHelp.html#BLATAlign" target="_blank">BLAT documentation</a> for more details. All of the following fields are required on each data line within a PSL file:</p> <ol> <li> <strong>matches</strong> - Number of bases that match that aren't repeats</li> <li> <strong>misMatches</strong> - Number of bases that don't match</li>