b44df11903f0c8537dc9d716df324906bc89f92b lrnassar Thu Jun 15 13:21:32 2023 -0700 Adding documentation supporting snakes rearrangement display, refs #31241 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 0ea7326..e97207e 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -270,31 +270,33 @@ 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 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 +documentation</a> for more details. PSL data tracks can also be visualized in +<a href="../goldenPath/help/chain.html#rearrangement" target="_blank">rearrangement +display mode</a>. 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> <li> <strong>repMatches</strong> - Number of bases that match but are part of repeats</li> <li> <strong>nCount</strong> - Number of "N" bases</li> <li> <strong>qNumInsert</strong> - Number of inserts in query</li> <li> <strong>qBaseInsert</strong> - Number of bases inserted in query</li> <li>