43efb3af4a3efe8d5f5b8e8a4e8464337a75790c
brianlee
  Thu May 16 14:54:20 2019 -0700
Updating interact help page to show interactUp and correct useScore=on and add image refs #23299

diff --git src/hg/htdocs/goldenPath/help/interact.html src/hg/htdocs/goldenPath/help/interact.html
index f823d91..410e232 100755
--- src/hg/htdocs/goldenPath/help/interact.html
+++ src/hg/htdocs/goldenPath/help/interact.html
@@ -163,46 +163,51 @@
 </ol>
 <p>
 After the file loads in the Genome Browser, you should see four interactions displayed on 
 chromosome 3.  Two of the interactions
 have both interacting regions in the browser view, and two have a single region. One of these 
 interacts across chromosomes (with a region on chromosome 20), and the other with a region 
 outside of the browser window (indicated by rectangular connector).
 The darkness of the interaction indicates the strength of the interaction.
 </p>
 
 <a name="example3"></a>
 <h6>Example #3</h6>
 <p>
 In this example, you will create a bigInteract track out of an existing bigInteract format file,
 located on the UCSC Genome Browser http server. This file contains data for the hg19 assembly.
+This example also contains the  <a href="./trackDb/trackDbHub.html#interactUp"
+target="_blank"><code>interactUp=true</code></a> setting to flip the arcs of the interact display.</p>
 </p>
 
 <p>
 To create a custom track using this file:
 <ol>
    <li>Construct a track line referencing the file and set the browser position to show region 
        of interest in the file:
    <pre><code>
-track type=bigInteract name=&quot;interact Example Three&quot; description=&quot;A bigInteract file&quot; useScore=true visibility=full bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/interact/interactExample3.inter.bb
+track type=bigInteract interactUp=true name=&quot;interact Example Three&quot; description=&quot;A bigInteract file&quot; useScore=on visibility=full bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/interact/interactExample3.inter.bb
 browser position chr3:63,820,967-63,880,091
    </code></pre></li>
    <li>Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg19">custom track management 
    page</a> for the human assembly hg19. </li>
    <li>Click the &quot;submit&quot; button.</li>
 </ol>
 </p>
+<ol>
+<img width="1080" height="148" src="../../images/interactExample3.png">
+</ol>
 <p>
 After the file loads in the Genome Browser, you should see a number of curved interactions, 
 colored black.
 </p>
 
 <a name="example4"></a>
 <h6>Example #4</h6>
 <p>
 In this example, you will use an example BED file to create a bigInteract file,
 allowing the data to be remotely accessed and exist within a track hub.  The track settings for 
 bigInteract on a hub can be viewed <a href="./trackDb/trackDbHub.html#bigInteract">here</a>.
 </p>
 <ol>
    <li>Download the example file <a href="examples/interact/interactExample4.inter.bed">here</a>. </li>
    <li>Download the <em>fetchChromSizes</em> and <em>bedToBigBed</em> programs from the
@@ -215,31 +220,31 @@
    data set&quot; for any assembly). For example, the <em>hg19.chrom.sizes</em> file for the hg19
    database is located at
    <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes" 
    target="_blank">http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes</a>.</li>
    <li>Save the autoSql file <a href="examples/interact/interact.as">interact.as</a> to your computer.
        If you want the column labels to reflect non-directional interactions, you can change the 
        default variable names from 'source...' and 'target...' to 'region1...' and 'region2...'.</li>
    <li>Run bedToBigBed to create the bigInteract file:
    <pre><code>
 bedToBigBed -as=interact.as -type=bed5+13 interactExample4.inter.bed hg19.chrom.sizes interactExample4.inter.bb
    </code></pre></li>
    <li>Move the newly constructed bigInteract file to a web accessible http, https, or ftp location.</li>
    <li>Construct a custom track line with a bigDataUrl parameter pointing to the newly created
    bigInteract file.
    <pre><code>
-track type=bigInteract name="interact Example Four" description="A bigInteract file" useScore=true bigDataUrl=<your URL>/interactExample4.inter.bb visibility=pack 
+track type=bigInteract name="interact Example Four" description="A bigInteract file" useScore=on bigDataUrl=<your URL>/interactExample4.inter.bb visibility=pack 
 browser position chr3:63,820,967-63,880,091
    </code></pre>
    <li>To fully take advantage of creating a bigInteract file, create a <a href="hgTrackHubHelp.html">Track Hub</a> and
    use a stanza such as the following:
    <pre><code>
 track exampleInteractTrack
 type bigInteract
 visibility full
 shortLabel exInteract
 longLabel Example interact track
 spectrum on
 scoreMin 175
 maxHeightPixels 300:150:20
 bigDataUrl interactExample4.inter.bb
    </code></pre>