From 5121e11190bfa470a14e3975caabfd0b0b205e57 Mon Sep 17 00:00:00 2001
From: Will Bradshaw <wjbradshaw1@gmail.com>
Date: Thu, 12 Oct 2023 18:01:35 -0400
Subject: [PATCH] Corrected date on adapter removal notebook

---
 docs/index.html                                        |  4 ++--
 docs/notebooks/2023-10-12_fastp-vs-adapterremoval.html | 10 +++++-----
 docs/search.json                                       |  2 +-
 notebooks/2023-10-12_fastp-vs-adapterremoval.qmd       |  6 +++---
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/docs/index.html b/docs/index.html
index a0cd625..9c7d597 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -129,7 +129,7 @@
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-listing-date-sort="1697860800000" data-listing-file-modified-sort="1697146749039" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="12">
+<div class="quarto-post image-right" data-index="0" data-listing-date-sort="1697083200000" data-listing-file-modified-sort="1697148076503" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="12">
 <div class="thumbnail">
 <p><a href="./notebooks/2023-10-12_fastp-vs-adapterremoval.html"> <p class="card-img-top"><img src="notebooks/2023-10-12_fastp-vs-adapterremoval_files/figure-html/unnamed-chunk-2-1.png"  class="thumbnail-image card-img"/></p> </a></p>
 </div>
@@ -146,7 +146,7 @@ <h3 class="no-anchor listing-title">
 <div class="metadata">
 <a href="./notebooks/2023-10-12_fastp-vs-adapterremoval.html">
 <div class="listing-date">
-Oct 21, 2023
+Oct 12, 2023
 </div>
 </a>
 </div>
diff --git a/docs/notebooks/2023-10-12_fastp-vs-adapterremoval.html b/docs/notebooks/2023-10-12_fastp-vs-adapterremoval.html
index d72d282..d2cd379 100644
--- a/docs/notebooks/2023-10-12_fastp-vs-adapterremoval.html
+++ b/docs/notebooks/2023-10-12_fastp-vs-adapterremoval.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.450">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Will Bradshaw">
-<meta name="dcterms.date" content="2023-10-21">
+<meta name="dcterms.date" content="2023-10-12">
 <title>Will’s Public NAO Notebook - Comparing FASTP and AdapterRemoval for MGS pre-processing</title>
 <style>
 code{white-space: pre-wrap;}
@@ -131,7 +131,7 @@
       <div>
       <div class="quarto-title-meta-heading">Published</div>
       <div class="quarto-title-meta-contents">
-        <p class="date">October 21, 2023</p>
+        <p class="date">October 12, 2023</p>
       </div>
     </div>
     
@@ -663,7 +663,7 @@
 <span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Comparing FASTP and AdapterRemoval for MGS pre-processing"</span></span>
 <span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="an">subtitle:</span><span class="co"> "Two tools -- how do they perform?"</span></span>
 <span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> "Will Bradshaw"</span></span>
-<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> 2023-10-21</span></span>
+<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> 2023-10-12</span></span>
 <span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span></span>
 <span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co">  html:</span></span>
 <span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="co">    code-fold: true</span></span>
@@ -690,7 +690,7 @@
 <span id="cb10-31"><a href="#cb10-31" aria-hidden="true" tabindex="-1"></a>To carry out this test, I selected three pairs of raw Illumina FASTQC files, corresponding to one sample each from two different published studies as well as one dataset provided to us by Marc Johnson:</span>
 <span id="cb10-32"><a href="#cb10-32" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb10-33"><a href="#cb10-33" aria-hidden="true" tabindex="-1"></a>| Study                        | Bioproject                                                        | Sample      |</span>
-<span id="cb10-34"><a href="#cb10-34" aria-hidden="true" tabindex="-1"></a>|------------------------------|-------------------------------------------------------------------|-------------|</span>
+<span id="cb10-34"><a href="#cb10-34" aria-hidden="true" tabindex="-1"></a>|-----------------|----------------------------------------|---------------|</span>
 <span id="cb10-35"><a href="#cb10-35" aria-hidden="true" tabindex="-1"></a>| Rothman et al. (2021)        | <span class="co">[</span><span class="ot">PRJNA729801</span><span class="co">](https://www.ebi.ac.uk/ena/browser/view/PRJNA729801)</span> | SRR19607374 |</span>
 <span id="cb10-36"><a href="#cb10-36" aria-hidden="true" tabindex="-1"></a>| Crits-Cristoph et al. (2021) | <span class="co">[</span><span class="ot">PRJNA661613</span><span class="co">](https://www.ebi.ac.uk/ena/browser/view/PRJNA661613)</span> | SRR23998357 |</span>
 <span id="cb10-37"><a href="#cb10-37" aria-hidden="true" tabindex="-1"></a>| Johnson (2023)               | N/A                                                               | COMO4       |</span>
@@ -774,7 +774,7 @@
 <span id="cb10-117"><a href="#cb10-117" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb10-118"><a href="#cb10-118" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>As previously observed, the raw data has very high duplicate levels, with only \~26% of sequences estimated by FASTQC to remain after deduplication. Increasing the comparison window to 100bp (from a default of 50bp) increases this to \~35%. Neither tool has much effect on this number -- unsurprisingly, since neither carried out deduplication.</span>
 <span id="cb10-119"><a href="#cb10-119" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb10-120"><a href="#cb10-120" aria-hidden="true" tabindex="-1"></a><span class="ss">-    </span>Finally, adapter removal. Unsurprisingly, the raw data shows substantial adapter content. AdapterRemoval does a good job of removing adapters, resulting in a "pass" grade from FASTQC. Surprisingly, despite trimming adapters from fewer reads, fastp does even better (according to FASTQC) at removing adapters.</span>
+<span id="cb10-120"><a href="#cb10-120" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>Finally, adapter removal. Unsurprisingly, the raw data shows substantial adapter content. AdapterRemoval does a good job of removing adapters, resulting in a "pass" grade from FASTQC. Surprisingly, despite trimming adapters from fewer reads, fastp does even better (according to FASTQC) at removing adapters.</span>
 <span id="cb10-121"><a href="#cb10-121" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb10-122"><a href="#cb10-122" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>The images below show raw, fastp, and AR adapter content:</span>
 <span id="cb10-123"><a href="#cb10-123" aria-hidden="true" tabindex="-1"></a></span>
diff --git a/docs/search.json b/docs/search.json
index 3cbeb05..40d0125 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -32,7 +32,7 @@
     "href": "index.html",
     "title": "Will's Public NAO Notebook",
     "section": "",
-    "text": "Comparing FASTP and AdapterRemoval for MGS pre-processing\n\n\nTwo tools – how do they perform?\n\n\n\n\n\n\nOct 21, 2023\n\n\n\n\n\n\n  \n\n\n\n\nHow does Element AVITI sequencing work?\n\n\nFindings of a shallow investigation\n\n\n\n\n\n\nOct 11, 2023\n\n\n\n\n\n\n  \n\n\n\n\nExtraction experiment 2: high-level results & interpretation\n\n\nComparing RNA yields and quality across extraction kits for settled solids\n\n\n\n\n\n\nSep 21, 2023\n\n\n\n\n\n\nNo matching items"
+    "text": "Comparing FASTP and AdapterRemoval for MGS pre-processing\n\n\nTwo tools – how do they perform?\n\n\n\n\n\n\nOct 12, 2023\n\n\n\n\n\n\n  \n\n\n\n\nHow does Element AVITI sequencing work?\n\n\nFindings of a shallow investigation\n\n\n\n\n\n\nOct 11, 2023\n\n\n\n\n\n\n  \n\n\n\n\nExtraction experiment 2: high-level results & interpretation\n\n\nComparing RNA yields and quality across extraction kits for settled solids\n\n\n\n\n\n\nSep 21, 2023\n\n\n\n\n\n\nNo matching items"
   },
   {
     "objectID": "notebooks/2023-10-12_fastp-vs-adapterremoval.html",
diff --git a/notebooks/2023-10-12_fastp-vs-adapterremoval.qmd b/notebooks/2023-10-12_fastp-vs-adapterremoval.qmd
index c2af170..69db036 100644
--- a/notebooks/2023-10-12_fastp-vs-adapterremoval.qmd
+++ b/notebooks/2023-10-12_fastp-vs-adapterremoval.qmd
@@ -2,7 +2,7 @@
 title: "Comparing FASTP and AdapterRemoval for MGS pre-processing"
 subtitle: "Two tools -- how do they perform?"
 author: "Will Bradshaw"
-date: 2023-10-21
+date: 2023-10-12
 format:
   html:
     code-fold: true
@@ -29,7 +29,7 @@ The first major step in our current MGS pipeline uses AdapterRemoval to automati
 To carry out this test, I selected three pairs of raw Illumina FASTQC files, corresponding to one sample each from two different published studies as well as one dataset provided to us by Marc Johnson:
 
 | Study                        | Bioproject                                                        | Sample      |
-|------------------------------|-------------------------------------------------------------------|-------------|
+|-----------------|----------------------------------------|---------------|
 | Rothman et al. (2021)        | [PRJNA729801](https://www.ebi.ac.uk/ena/browser/view/PRJNA729801) | SRR19607374 |
 | Crits-Cristoph et al. (2021) | [PRJNA661613](https://www.ebi.ac.uk/ena/browser/view/PRJNA661613) | SRR23998357 |
 | Johnson (2023)               | N/A                                                               | COMO4       |
@@ -113,7 +113,7 @@ g_rothman
 
 -   As previously observed, the raw data has very high duplicate levels, with only \~26% of sequences estimated by FASTQC to remain after deduplication. Increasing the comparison window to 100bp (from a default of 50bp) increases this to \~35%. Neither tool has much effect on this number -- unsurprisingly, since neither carried out deduplication.
 
--    Finally, adapter removal. Unsurprisingly, the raw data shows substantial adapter content. AdapterRemoval does a good job of removing adapters, resulting in a "pass" grade from FASTQC. Surprisingly, despite trimming adapters from fewer reads, fastp does even better (according to FASTQC) at removing adapters.
+-   Finally, adapter removal. Unsurprisingly, the raw data shows substantial adapter content. AdapterRemoval does a good job of removing adapters, resulting in a "pass" grade from FASTQC. Surprisingly, despite trimming adapters from fewer reads, fastp does even better (according to FASTQC) at removing adapters.
 
 -   The images below show raw, fastp, and AR adapter content: