From 5f0183fd184e823ca20840685c8f326421ff00ed Mon Sep 17 00:00:00 2001
From: mconomos <mconomos@uw.edu>
Date: Wed, 5 Jun 2024 23:09:33 -0700
Subject: [PATCH] update tutorial 7

---
 07_STAAR.Rmd  | 6 +++---
 07_STAAR.html | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/07_STAAR.Rmd b/07_STAAR.Rmd
index 3a91591..ac1ba8a 100644
--- a/07_STAAR.Rmd
+++ b/07_STAAR.Rmd
@@ -106,7 +106,7 @@ Note: we will utilize the default allele frequency setting (max MAF $1\%$), and
 
 The analysis will take ~10 minutes to run. You can find your analysis in the Tasks menu of your Project to check on its progress and see the results once it has completed. 
 
-The output from this task is `<output_prefix>.Rdata`, which contains the STAAR association results.
+The output from this task is `<output_prefix>_chr<CHR>.Rdata`, which contains the STAAR association results.
 
 You can find the expected output of this analysis by looking at the existing task `14 STAARexercise Sliding Window 5kb Chr19` in the Tasks menu of your Project. The output files are available in the Project, so you do not need to wait for your analysis to finish to look at the output.
 
@@ -118,10 +118,10 @@ The output file for these association tests using STAAR is an `.RData` file. To
   - Click: Apps > `STAARpipelineSummary VarSet` > Run
   - Specify the Inputs:
     - Annotation name catalog: `Annotation_name_catalog.csv`
-    - Input array results: `STAAR_region_sliding_5kb_chr19.Rdata`
+    - Input array results: `STAAR_region_sliding_5kb_chr19_chr19.Rdata`
   - Specify App Settings: 
     - Output file prefix: "STAAR_region_sliding_5kb_chr19" (or any other string to name the output file)
-    - Prefix of input results: "STAAR_region_sliding_5kb_chr19"
+    - Prefix of input results: "STAAR_region_sliding_5kb_chr19_chr"
     - Test type: Sliding_Window
   - Click: Run
 
diff --git a/07_STAAR.html b/07_STAAR.html
index b654126..2a7c25b 100644
--- a/07_STAAR.html
+++ b/07_STAAR.html
@@ -546,8 +546,8 @@ <h2>Exercise 7.3 (Application)</h2>
 in the Tasks menu of your Project to check on its progress and see the
 results once it has completed.</p>
 <p>The output from this task is
-<code>&lt;output_prefix&gt;.Rdata</code>, which contains the STAAR
-association results.</p>
+<code>&lt;output_prefix&gt;_chr&lt;CHR&gt;.Rdata</code>, which contains
+the STAAR association results.</p>
 <p>You can find the expected output of this analysis by looking at the
 existing task <code>14 STAARexercise Sliding Window 5kb Chr19</code> in
 the Tasks menu of your Project. The output files are available in the
@@ -569,13 +569,13 @@ <h2>Exercise 7.4 (Application)</h2>
 <li>Annotation name catalog:
 <code>Annotation_name_catalog.csv</code></li>
 <li>Input array results:
-<code>STAAR_region_sliding_5kb_chr19.Rdata</code></li>
+<code>STAAR_region_sliding_5kb_chr19_chr19.Rdata</code></li>
 </ul></li>
 <li>Specify App Settings:
 <ul>
 <li>Output file prefix: “STAAR_region_sliding_5kb_chr19” (or any other
 string to name the output file)</li>
-<li>Prefix of input results: “STAAR_region_sliding_5kb_chr19”</li>
+<li>Prefix of input results: “STAAR_region_sliding_5kb_chr19_chr”</li>
 <li>Test type: Sliding_Window</li>
 </ul></li>
 <li>Click: Run</li>