ef932f66f1608a5cbe6840662be9aa1b67ae95bd brianlee Fri Apr 16 09:27:27 2021 -0700 Adding a PCR forward/reverse sequence example as proof of concept for Assembly Hub PCR after Max note in Progress Report about working on laptops. diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 91f4c5f..ca96c17 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -219,17 +219,23 @@ <p> Run the two gfServer commands to start the blat servers:</p> <pre><code>gfServer start localhost 17777 -trans -mask araTha1.2bit & gfServer start localhost 17779 -stepSize=5 araTha1.2bit & </code></pre> <p> <strong>STEP 8.</strong> Load this plant assembly hub by using this URL and selecting it under the "group" category where "Plant araTha1" displays:</p> <pre><code><a href="http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txt" target="_blank">http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></code></pre> <p> On the blat page, <code><a href="http://127.0.0.1:1234/cgi-bin/hgBlat" target="_blank">http://127.0.0.1:1234/cgi-bin/hgBlat</a></code>, you can now select the <em>Arabidopsis thaliana</em> assembly and blat plant amino acid sequences, like <code>IYQTRENKYIIGEIQITESERDRRRSSLPGNH</code> or DNA sequences, like <code>TAAGTAAAAAATAATATGATTAAGACTAATAAATCTTAATAGTTAATACT</code>. - +</p> +<p>On the PCR page, <code><a href="http://127.0.0.1:1234/cgi-bin/hgPcr" +target="_blank">http://127.0.0.1:1234/cgi-bin/hgPcr</a></code>, you can now select the +<em>Arabidopsis thaliana</em> genome and enter a forward primer such as +<code>TAGGTCTGCACCTGTGGTTCAAAATTTT</code> and a reverse primer such as +<code>CAATACAAGTCAACATTTTAGCGCCGAGA</code> and click the "Flip Reverse Primer" +box and then click submit to find matches on the assembly.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->