version_1.0.0

Author: Geize

Qiime2_wrap.html

@@ -370,7 +370,7 @@ <h1><strong>16S rRNA analysis pipeline</strong></h1>
 <p><br /></p>
 <p>The propose of this page is the reproducibility of the 16S data
 described in my publications
-(e.g.,<a href=" https://journals.asm.org/doi/abs/10.1128/AEM.00199-20">Tomazetto
+(e.g.,<a href="https://journals.asm.org/doi/abs/10.1128/AEM.00199-20">Tomazetto
 et al.</a>) or those are coming up soon. If you are looking for a
 tutorial,
 <a href="&lt;https://docs.qiime2.org/2022.2/tutorials/moving-pictures/">
@@ -386,6 +386,7 @@ <h1><strong>16S rRNA analysis pipeline</strong></h1>
 <li>Run the activate step.</li>
 <li>Test if qiime2 successfully activated 🔥- very important step.</li>
 </ul>
+<!-- -->
 <pre><code>qiime --help</code></pre>
 <p><br /></p>
 <ul>
@@ -417,12 +418,12 @@ <h1><strong>16S rRNA analysis pipeline</strong></h1>
 instructions - very fancy. 😁</p>
 <pre><code>(base) ➜ ~  python Write_manifestFile.py -help</code></pre>
 <p><br /> <strong>5. Processing the data.</strong></p>
-<p>Once you have the manifest file, <code>DrT_Qiime2.sh</code>, and of
-course, fastq.gz in a directory, you can run the script. All the steps
-are wrapped in a single script, including the importing the data,
-denoising, trimming, joining, table ASVs, tree, and basic diverstiy
-analysis. The script also has the steps to convert QIIME2 artifacts into
-visualization files, which you can view using qiime tools view or
+<p>Once you have the manifest file, <code>DrT_Qiime2.sh</code>, and
+fastq.gz in a directory, you can run the script. All the steps are
+wrapped in a single script, including the importing the data, denoising,
+trimming, joining, table ASVs, tree, and basic diverstiy analysis. The
+script also has the steps to convert QIIME2 artifacts into visualization
+files, which you can view using qiime tools view or
 <a href="https://view.qiime2.org">here</a>.</p>
 <p>Check out the output files and directories!</p>
 <p>
@@ -439,9 +440,9 @@ <h1><strong>16S rRNA analysis pipeline</strong></h1>
 after each step.</p>
 <p><br /></p>
 <p><strong>6. Plotting some graphics.</strong></p>
-<p>Here, you also find a R script to plot some graphics. Of course, you
-can plot different graphics emphasizing “little this or little that”. It
-is up to you.</p>
+<p>Here, you also find a R script to plot some graphics. You can plot
+different graphics emphasizing “little this or little that”. It is up to
+you.</p>
 <p><br /> All the best for us! 🤓</p>
 <hr />
 </div>

README.html

@@ -2,7 +2,7 @@
 
 <br/>
 
-The propose of this page is the reproducibility of the 16S data described in my publications (e.g.,<a href=" https://journals.asm.org/doi/abs/10.1128/AEM.00199-20">Tomazetto et al.</a>) or those are coming up soon. If you are looking for a tutorial, <a href="<https://docs.qiime2.org/2022.2/tutorials/moving-pictures/"> here</a> is the best one you can have.
+The propose of this page is the reproducibility of the 16S data described in my publications (e.g.,<a href="https://journals.asm.org/doi/abs/10.1128/AEM.00199-20">Tomazetto et al.</a>) or those are coming up soon. If you are looking for a tutorial, <a href="<https://docs.qiime2.org/2022.2/tutorials/moving-pictures/"> here</a> is the best one you can have.
 
 However, you are more than welcome to reach out to me if you need help. Do not worry, I won't jump into your work. But I'll be glad if you can cite one of my works as a reference. 😊
 
@@ -12,9 +12,9 @@ However, you are more than welcome to reach out to me if you need help. Do not w
 -   Run the activate step.
 -   Test if qiime2 successfully activated 🔥- very important step.
 
-```
-qiime --help
-```
+<!-- -->
+
+    qiime --help
 
 <br/>
 
@@ -25,9 +25,7 @@ qiime --help
 
 **2. Transfer the fastq.gz files from your computer/HDD to the server.**
 
-```
-(base) ➜ ~  scp data/*.fastq.gz  mylogin@login:/home/geize/16S/
-```
+    (base) ➜ ~  scp data/*.fastq.gz  mylogin@login:/home/geize/16S/
 
 <br/>
 
@@ -39,25 +37,21 @@ I usually create metadata files according to the project and what is need to com
 
 🔥**Important note.**<br> Do not forget to save the file as tab-delimited - it's the best option. Validate your metadata using a Keemei.
 
-```
-#SampleID   Description   Condition   ...
-Sample01    Soil    Ref      ...
-Sample02    Cons    A        ...
-Sample03    Cons    B        ...
-and dadada...
-```
+    #SampleID   Description   Condition   ...
+    Sample01    Soil    Ref      ...
+    Sample02    Cons    A        ...
+    Sample03    Cons    B        ...
+    and dadada...
 
 <br/> **4.Back to the server to create the manifest file.**
 
 The following python script can help you to create a manifest file from any directory. Just type the command bellow to get more instructions - very fancy. 😁
 
-```
-(base) ➜ ~  python Write_manifestFile.py -help
-```
+    (base) ➜ ~  python Write_manifestFile.py -help
 
 <br/> **5. Processing the data.**
 
-Once you have the manifest file, `DrT_Qiime2.sh`, and of course, fastq.gz in a directory, you can run the script. All the steps are wrapped in a single script, including the importing the data, denoising, trimming, joining, table ASVs, tree, and basic diverstiy analysis. The script also has the steps to convert QIIME2 artifacts into visualization files, which you can view using qiime tools view or <a href="https://view.qiime2.org">here</a>.
+Once you have the manifest file, `DrT_Qiime2.sh`, and fastq.gz in a directory, you can run the script. All the steps are wrapped in a single script, including the importing the data, denoising, trimming, joining, table ASVs, tree, and basic diverstiy analysis. The script also has the steps to convert QIIME2 artifacts into visualization files, which you can view using qiime tools view or <a href="https://view.qiime2.org">here</a>.
 
 Check out the output files and directories!
 
@@ -75,7 +69,7 @@ The `qiime tools validate` command was added after some critical steps. Open the
 
 **6. Plotting some graphics.**
 
-Here, you also find a R script to plot some graphics. Of course, you can plot different graphics emphasizing "little this or little that". It is up to you.
+Here, you also find a R script to plot some graphics. You can plot different graphics emphasizing "little this or little that". It is up to you.
 
 <br/> All the best for us! 🤓