From 7433203cd089882b71f4290912ede220e60b5c53 Mon Sep 17 00:00:00 2001
From: Kristina Hanspers <kristina.hanspers@gladstone.ucsf.edu>
Date: Mon, 28 Oct 2024 08:28:51 -0700
Subject: [PATCH] Update index.html

final updates
---
 protocols/rna-seq-data-analysis/index.html | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/protocols/rna-seq-data-analysis/index.html b/protocols/rna-seq-data-analysis/index.html
index bebada4c..09fe78b9 100644
--- a/protocols/rna-seq-data-analysis/index.html
+++ b/protocols/rna-seq-data-analysis/index.html
@@ -129,8 +129,7 @@ <h1>Data Integration</h1>
     <p>Next we will import the RNA-Seq data and use them to create a visualization.</p>
     <ul>
     <li>Load the downloaded <b>rna-seq-data-cytoscape.csv</b> file under <highlight>File</highlight> menu by selecting <highlight>Import &rarr; Table from File....</highlight>. Alternatively, drag and drop the data file directly onto the <highlight>Node Table</highlight>.</li>
-    <li>In <highlight>Advanced Options...</highlight>, in the <highlight>Ignore Lines Starting With</highlight> field, enter <b>#</b>, to exclude the additional lines at the beginning of the data file.</li>
-	<li>Select the <b>query term</b> column as the <b>Key column for Network</b> and select the <b>Gene Name</b> column as the key column by clicking on the header and selecting the key symbol.</li>
+    <li>Select the <b>query term</b> column as the <b>Key column for Network</b> and select the <b>Gene Name</b> column as the key column by clicking on the header and selecting the key symbol.</li>
     <li>Click <highlight>OK</highlight> to import. Two new columns of data will be added to the <highlight>Node Table</highlight>.</li>
 </ul><br /><br />
     <div style="width:38%;float:left">
@@ -160,7 +159,7 @@ <h1>Visualization</h1>
         <li>For node <highlight>Fill Color</highlight>, create a continuous mapping for <highlight>Fold Change</highlight>. Keep the default red-blue color palette.</li>
         <!-- <li>Double-cllick the color mapping to open the <highlight>Continuous Mapping Editor</highlight> and click the <highlight>Current Palette</highlight>. Select the ColorBrewer <b>yellow-orange-red shades</b> gradient.</li> -->
         <li>Finally, for node <highlight>Label</highlight>, set a passthrough mapping for <highlight>display name</highlight>.</li>
-        <li>Save your new visualization under <highlight>Copy Style...</highlight> in the <highlight>Options</highlight> menu of the <highlight>Style</highlight> interface, and name it <b>de genes up</b>.</li>
+        <li>Save your new visualization under <highlight>Copy Style...</highlight> in the <highlight>Options</highlight> menu of the <highlight>Style</highlight> interface, and name it <b>de genes</b>.</li>
     </ul>
     <img class="plain" src="style-viz2.png" style="height:450px">