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docs/index.html

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 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
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+<div class="quarto-post image-right" data-index="0" data-listing-date-sort="1698897600000" data-listing-file-modified-sort="1698943032000" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="14">
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 <p><a href="./notebooks/2023-11-02_project-runway-comparison.html"> <p class="card-img-top"><img src="notebooks/2023-11-02_project-runway-comparison_files/figure-html/unnamed-chunk-2-1.png"  class="thumbnail-image card-img"/></p> </a></p>
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docs/notebooks/2023-11-02_project-runway-comparison.html

@@ -289,7 +289,7 @@
 </li>
 <li><p>For difference 2 (ribodepletion) results here are equivocal. The single read pair I inspected that got removed during ribodepletion appears to include both a true ribosomal read and a true viral read. I think some internal discussion is needed to decide how to handle these cases.</p></li>
 <li>
-<p>For difference 3 (deduplication) I updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).</p>
+<p>For difference 3 (deduplication) I initially updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).</p>
 <ul>
 <li><p>However, I found an option for Clumpify which addresses this issue, at least in this case. Specifically, one can configure Clumpify to unpair reads, perform deduplication on the forward and reverse reads all together, and then restore pairing. This successfully removes this class of duplicates.</p></li>
 <li><p>I’m a little worried that this approach might sometimes cause complete loss of all duplicate reads (rather than all-but-one-pair) when the best-quality duplicate differs between forward and reverse reads. I tried this out by artificially modifying the quality scores for the duplicate reads from D23-13405-2, and this doesn’t seem to be the case at least in this instance: when quality across read pairs was concordant, I was able to control which read pair survived as expected, and when it was discordant, one read pair survived anyway. Still, this remains a niggling doubt.</p></li>
@@ -756,7 +756,7 @@
 <span id="cb3-176"><a href="#cb3-176" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-177"><a href="#cb3-177" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>For difference 2 (ribodepletion) results here are equivocal. The single read pair I inspected that got removed during ribodepletion appears to include both a true ribosomal read and a true viral read. I think some internal discussion is needed to decide how to handle these cases.</span>
 <span id="cb3-178"><a href="#cb3-178" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb3-179"><a href="#cb3-179" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>For difference 3 (deduplication) I updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).</span>
+<span id="cb3-179"><a href="#cb3-179" aria-hidden="true" tabindex="-1"></a><span class="ss">-   </span>For difference 3 (deduplication) I initially updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).</span>
 <span id="cb3-180"><a href="#cb3-180" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-181"><a href="#cb3-181" aria-hidden="true" tabindex="-1"></a><span class="ss">    -   </span>However, I found an option for Clumpify which addresses this issue, at least in this case. Specifically, one can configure Clumpify to unpair reads, perform deduplication on the forward and reverse reads all together, and then restore pairing. This successfully removes this class of duplicates.</span>
 <span id="cb3-182"><a href="#cb3-182" aria-hidden="true" tabindex="-1"></a></span>

notebooks/2023-11-02_project-runway-comparison.qmd

@@ -170,7 +170,7 @@ g_hit
 
 -   For difference 2 (ribodepletion) results here are equivocal. The single read pair I inspected that got removed during ribodepletion appears to include both a true ribosomal read and a true viral read. I think some internal discussion is needed to decide how to handle these cases.
 
--   For difference 3 (deduplication) I updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).
+-   For difference 3 (deduplication) I initially updated negatively about Clumpify, which appeared to be unable to handle duplicates where the forward and reverse reads in a pair are switched (this is also a case where FASTQC will be unable to detect these duplicates).
 
     -   However, I found an option for Clumpify which addresses this issue, at least in this case. Specifically, one can configure Clumpify to unpair reads, perform deduplication on the forward and reverse reads all together, and then restore pairing. This successfully removes this class of duplicates.