Added deduplication notebook

naobservatory · Oct 20, 2023 · 76e70e0 · 76e70e0
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Showing 14 changed files with 971 additions and 30 deletions.
diff --git a/data/2023-10-19_deduplication/duplicate-data.csv b/data/2023-10-19_deduplication/duplicate-data.csv
@@ -0,0 +1,19 @@
+dataset,sample,processing_stage,dedup_method,fastqc_pc_dup,fastqc_dup_test
+Johnson,COMO4,Preprocessed (FASTP),None,74.36,Failed
+Johnson,COMO4,Preprocessed (FASTP),Clumpify,24.19,Passed
+Johnson,COMO4,Preprocessed (FASTP),FASTP dedup,68.09,Failed
+Johnson,COMO4,Ribodepleted (BBDUK),None,69.72,Failed
+Johnson,COMO4,Ribodepleted (BBDUK),Clumpify,18.38,Passed
+Johnson,COMO4,Ribodepleted (BBDUK),FASTP dedup,59.78,Failed
+Rothman,SRR14530880,Preprocessed (FASTP),None,81.27,Failed
+Rothman,SRR14530880,Preprocessed (FASTP),Clumpify,27.9,Passed
+Rothman,SRR14530880,Preprocessed (FASTP),FASTP dedup,62.9,Failed
+Rothman,SRR14530880,Ribodepleted (BBDUK),None,78.79,Failed
+Rothman,SRR14530880,Ribodepleted (BBDUK),Clumpify,33,Warning
+Rothman,SRR14530880,Ribodepleted (BBDUK),FASTP dedup,63.2,Failed
+Crits-Christoph,SRR23998357,Preprocessed (FASTP),None,55.9,Failed
+Crits-Christoph,SRR23998357,Preprocessed (FASTP),Clumpify,10.64,Passed
+Crits-Christoph,SRR23998357,Preprocessed (FASTP),FASTP dedup,35.22,Warning
+Crits-Christoph,SRR23998357,Ribodepleted (BBDUK),None,53.1,Failed
+Crits-Christoph,SRR23998357,Ribodepleted (BBDUK),Clumpify,9.89,Passed
+Crits-Christoph,SRR23998357,Ribodepleted (BBDUK),FASTP dedup,32.07,Warning
diff --git a/docs/index.html b/docs/index.html
@@ -129,7 +129,29 @@
 
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+<p><a href="./notebooks/2023-10-19_deduplication.html"> <p class="card-img-top"><img src="notebooks/2023-10-19_deduplication_files/figure-html/unnamed-chunk-2-1.png"  class="thumbnail-image card-img"/></p> </a></p>
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+<div class="body">
+<a href="./notebooks/2023-10-19_deduplication.html">
+<h3 class="no-anchor listing-title">
+Comparing options for read deduplication
+</h3>
+<div class="listing-subtitle">
+
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+</a>
+</div>
+<div class="metadata">
+<a href="./notebooks/2023-10-19_deduplication.html">
+<div class="listing-date">
+Oct 19, 2023
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+</a>
+</div>
+</div>
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@@ -2,6 +2,7 @@
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