Merge pull request #2 from csc-training/IonTorrentJYU23

Add Ion Torrent exercises
csc-training · Aug 10, 2023 · cbe02f4 · cbe02f4
2 parents f7615b8 + 75ee8eb
commit cbe02f4
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diff --git a/docs/IonTorrent/Exercises_day2.html b/docs/IonTorrent/Exercises_day2.html
@@ -7,7 +7,7 @@
 
 
 
-    <title>Exercises_day2.knit</title>
+    <title>Exercises_IonTorrent_day2.knit</title>
 
         <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -864,10 +864,8 @@ <h3><strong>Getting the data into <code>phyloseq</code></strong></h3>
 <ol style="list-style-type: lower-roman">
 <li><p>Select the file <code>file.opti_mcc.shared</code> and in the
 <em>Selected files</em> choose the tab <em>Phenodata</em>.</p></li>
-<li><p>Remove the columns <code>chiptype</code>, <code>group</code> and
-<code>description</code> by clicking the <code>x</code>. Create new
-columns called <code>site</code> and <code>bagging</code> by clicking
-<code>+ Add column</code>.</p></li>
+<li><p>Create new columns called <code>site</code> and
+<code>bagging</code> by clicking <code>+ Add column</code>.</p></li>
 <li><p>Check how the sample names in the column <code>sample</code>
 start, and based on this enter the site codes <code>HP</code> and
 <code>KEK</code> in the column <code>site</code>. Next, check the

diff --git a/eLena_md/IonTorrent/Exercises_IonTorrent_day2.Rmd b/eLena_md/IonTorrent/Exercises_IonTorrent_day2.Rmd
@@ -40,7 +40,7 @@ The `Generate input files for phyloseq` tool produces a phenodata file (a file t
 
 i) Select the file `file.opti_mcc.shared` and in the *Selected files* choose the tab *Phenodata*.
 
-ii) Remove the columns `chiptype`, `group` and `description` by clicking the `x`. Create new columns called `site` and  `bagging` by clicking `+ Add column`. 
+ii) Create new columns called `site` and `bagging` by clicking `+ Add column`. 
 
 iii) Check how the sample names in the column `sample` start, and based on this enter the site codes `HP` and `KEK` in the column `site`. Next, check the characters after `HP`and `KEK` in the sample names. When the next character is c, fill in `control` in the column `bagging`. When the next characters are `ps`, fill in `bagged` in the column `bagging`.