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hds-sandbox · May 27, 2024 · b41b4d7 · b41b4d7
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-8fbb9ce5
+c9a80ecf
diff --git a/develop/02_experimental_planning.html b/develop/02_experimental_planning.html
@@ -73,17 +73,17 @@
 
 </head>
 
-<body class="nav-sidebar docked nav-fixed fullcontent">
+<body class="nav-sidebar docked nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
     <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
-    <a href="../index.html" class="navbar-brand navbar-brand-logo">
+    <a href="http://hds-sandbox.github.io/" class="navbar-brand navbar-brand-logo">
     <img src="../develop/img/logo.png" alt="" class="navbar-logo">
     </a>
-    <a class="navbar-brand" href="../index.html">
+    <a class="navbar-brand" href="http://hds-sandbox.github.io/">
     <span class="navbar-title">Bulk RNAseq data analysis</span>
     </a>
   </div>
@@ -142,7 +142,7 @@
   </nav>
 </header>
 <!-- content -->
-<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-full page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
         <div class="mt-2 flex-shrink-0 align-items-center">
@@ -171,15 +171,15 @@
 <!-- margin-sidebar -->
 
 <!-- main -->
-<main class="content" id="quarto-document-content">
+<main class="content column-page-right" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 </div>
 
 
 
-<div class="quarto-title-meta">
+<div class="quarto-title-meta column-page-right">
 
 
 
@@ -628,7 +628,7 @@ <h3 class="anchored" data-anchor-id="best-practices-regarding-batches">Best prac
   });
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
-      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course\/");
+      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
@@ -956,7 +956,7 @@ <h3 class="anchored" data-anchor-id="best-practices-regarding-batches">Best prac
   }
 });
 </script>
-<nav class="page-navigation">
+<nav class="page-navigation column-page-right">
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">

diff --git a/develop/03_data_explanation.html b/develop/03_data_explanation.html
@@ -73,17 +73,17 @@
 
 </head>
 
-<body class="nav-sidebar docked nav-fixed fullcontent">
+<body class="nav-sidebar docked nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
     <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
-    <a href="../index.html" class="navbar-brand navbar-brand-logo">
+    <a href="http://hds-sandbox.github.io/" class="navbar-brand navbar-brand-logo">
     <img src="../develop/img/logo.png" alt="" class="navbar-logo">
     </a>
-    <a class="navbar-brand" href="../index.html">
+    <a class="navbar-brand" href="http://hds-sandbox.github.io/">
     <span class="navbar-title">Bulk RNAseq data analysis</span>
     </a>
   </div>
@@ -142,7 +142,7 @@
   </nav>
 </header>
 <!-- content -->
-<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-full page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
         <div class="mt-2 flex-shrink-0 align-items-center">
@@ -171,7 +171,7 @@
 <!-- margin-sidebar -->
 
 <!-- main -->
-<main class="content" id="quarto-document-content">
+<main class="content column-page-right" id="quarto-document-content">
 
 
 
@@ -458,7 +458,7 @@ <h1>Dataset explanation</h1>
   });
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
-      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course\/");
+      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
@@ -786,7 +786,7 @@ <h1>Dataset explanation</h1>
   }
 });
 </script>
-<nav class="page-navigation">
+<nav class="page-navigation column-page-right">
   <div class="nav-page nav-page-previous">
       <a href="../develop/02_experimental_planning.html" class="pagination-link" aria-label="Experimental design considerations">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Experimental design considerations</span>

diff --git a/develop/04a_preprocessing.html b/develop/04a_preprocessing.html
@@ -114,10 +114,10 @@
     <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
-    <a href="../index.html" class="navbar-brand navbar-brand-logo">
+    <a href="http://hds-sandbox.github.io/" class="navbar-brand navbar-brand-logo">
     <img src="../develop/img/logo.png" alt="" class="navbar-logo">
     </a>
-    <a class="navbar-brand" href="../index.html">
+    <a class="navbar-brand" href="http://hds-sandbox.github.io/">
     <span class="navbar-title">Bulk RNAseq data analysis</span>
     </a>
   </div>
@@ -176,7 +176,7 @@
   </nav>
 </header>
 <!-- content -->
-<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-full page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
         <div class="mt-2 flex-shrink-0 align-items-center">
@@ -209,43 +209,9 @@
 </nav>
 <div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
-        <nav id="TOC" role="doc-toc" class="toc-active">
-    <h2 id="toc-title">On this page</h2>
-
-  <ul>
-  <li><a href="#rna-extraction-and-library-preparation" id="toc-rna-extraction-and-library-preparation" class="nav-link active" data-scroll-target="#rna-extraction-and-library-preparation">1. RNA Extraction and library preparation</a></li>
-  <li><a href="#sequencing-illumina" id="toc-sequencing-illumina" class="nav-link" data-scroll-target="#sequencing-illumina">2. Sequencing (Illumina)</a>
-  <ul class="collapse">
-  <li><a href="#sequencing-by-synthesis" id="toc-sequencing-by-synthesis" class="nav-link" data-scroll-target="#sequencing-by-synthesis">Sequencing-by-synthesis</a></li>
-  </ul></li>
-  <li><a href="#quality-control-of-raw-sequencing-data" id="toc-quality-control-of-raw-sequencing-data" class="nav-link" data-scroll-target="#quality-control-of-raw-sequencing-data">3. Quality control of raw sequencing data</a>
-  <ul class="collapse">
-  <li><a href="#quality-metrics" id="toc-quality-metrics" class="nav-link" data-scroll-target="#quality-metrics">Quality metrics</a></li>
-  </ul></li>
-  <li><a href="#read-filtering-and-trimming" id="toc-read-filtering-and-trimming" class="nav-link" data-scroll-target="#read-filtering-and-trimming">4. Read filtering and trimming</a>
-  <ul class="collapse">
-  <li><a href="#cutadapt" id="toc-cutadapt" class="nav-link" data-scroll-target="#cutadapt">Cutadapt</a></li>
-  <li><a href="#trim-galore" id="toc-trim-galore" class="nav-link" data-scroll-target="#trim-galore">Trim Galore</a></li>
-  </ul></li>
-  <li><a href="#quality-control-of-clean-sequencing-data" id="toc-quality-control-of-clean-sequencing-data" class="nav-link" data-scroll-target="#quality-control-of-clean-sequencing-data">5. Quality control of clean sequencing data</a></li>
-  <li><a href="#alignment" id="toc-alignment" class="nav-link" data-scroll-target="#alignment">6. Alignment</a>
-  <ul class="collapse">
-  <li><a href="#traditional-alignment-tools" id="toc-traditional-alignment-tools" class="nav-link" data-scroll-target="#traditional-alignment-tools">Traditional alignment tools</a></li>
-  <li><a href="#pseudoalignment" id="toc-pseudoalignment" class="nav-link" data-scroll-target="#pseudoalignment">Pseudoalignment</a></li>
-  </ul></li>
-  <li><a href="#quality-control-of-aligned-reads" id="toc-quality-control-of-aligned-reads" class="nav-link" data-scroll-target="#quality-control-of-aligned-reads">7. Quality control of aligned reads</a>
-  <ul class="collapse">
-  <li><a href="#qualimap" id="toc-qualimap" class="nav-link" data-scroll-target="#qualimap">Qualimap</a></li>
-  <li><a href="#dupradar" id="toc-dupradar" class="nav-link" data-scroll-target="#dupradar">dupRadar</a></li>
-  </ul></li>
-  <li><a href="#quantify-expression" id="toc-quantify-expression" class="nav-link" data-scroll-target="#quantify-expression">8. Quantify expression</a></li>
-  <li><a href="#aggregation-of-quality-control-checks" id="toc-aggregation-of-quality-control-checks" class="nav-link" data-scroll-target="#aggregation-of-quality-control-checks">9. Aggregation of quality control checks</a></li>
-  </ul>
-</nav>
-    </div>
+
 <!-- main -->
-<main class="content" id="quarto-document-content">
+<main class="content column-page-right" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
@@ -254,7 +220,7 @@ <h1 class="title">Preprocessing steps</h1>
 
 
 
-<div class="quarto-title-meta">
+<div class="quarto-title-meta column-page-right">
 
 
 
@@ -739,7 +705,7 @@ <h2 class="anchored" data-anchor-id="aggregation-of-quality-control-checks">9. A
   });
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
-      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course\/");
+      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
@@ -1067,7 +1033,7 @@ <h2 class="anchored" data-anchor-id="aggregation-of-quality-control-checks">9. A
   }
 });
 </script>
-<nav class="page-navigation">
+<nav class="page-navigation column-page-right">
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">

diff --git a/develop/04b_pipelines.html b/develop/04b_pipelines.html
@@ -108,17 +108,17 @@
 
 </head>
 
-<body class="nav-sidebar docked nav-fixed fullcontent">
+<body class="nav-sidebar docked nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
     <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
-    <a href="../index.html" class="navbar-brand navbar-brand-logo">
+    <a href="http://hds-sandbox.github.io/" class="navbar-brand navbar-brand-logo">
     <img src="../develop/img/logo.png" alt="" class="navbar-logo">
     </a>
-    <a class="navbar-brand" href="../index.html">
+    <a class="navbar-brand" href="http://hds-sandbox.github.io/">
     <span class="navbar-title">Bulk RNAseq data analysis</span>
     </a>
   </div>
@@ -177,7 +177,7 @@
   </nav>
 </header>
 <!-- content -->
-<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
+<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-full page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
         <div class="mt-2 flex-shrink-0 align-items-center">
@@ -212,7 +212,7 @@
 <!-- margin-sidebar -->
 
 <!-- main -->
-<main class="content" id="quarto-document-content">
+<main class="content column-page-right" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
@@ -221,7 +221,7 @@ <h1 class="title">Nextflow &amp; nf-core pipelines</h1>
 
 
 
-<div class="quarto-title-meta">
+<div class="quarto-title-meta column-page-right">
 
 
 
@@ -883,7 +883,7 @@ <h4 class="anchored" data-anchor-id="pseudoaligner">7. <code>pseudoaligner</code
   });
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
-      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course\/");
+      var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/bulk_RNAseq_course");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
@@ -1211,7 +1211,7 @@ <h4 class="anchored" data-anchor-id="pseudoaligner">7. <code>pseudoaligner</code
   }
 });
 </script>
-<nav class="page-navigation">
+<nav class="page-navigation column-page-right">
   <div class="nav-page nav-page-previous">
       <a href="../develop/04a_preprocessing.html" class="pagination-link" aria-label="Preprocessing steps">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Preprocessing steps</span>