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lecture_notes:05-15-2015

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lecture_notes:05-15-2015 [2015/05/18 15:02]
gepoliano
lecture_notes:05-15-2015 [2015/05/18 15:11] (current)
gepoliano
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   * Pre-processed adapter trimming ​   * Pre-processed adapter trimming ​
   * Duplicate-removal is later than indexing   * Duplicate-removal is later than indexing
-  * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed ​+  * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed 
 +  * The overall duplication level is a problem 
 +  * Each datset was generated independently 
 +  * Then, removing duplicates should be done apart for each dataset 
 +  * The dataset is very complicated - there is big duplication rate across the dataset the group has 
 +  * Merging indexes - planning on pulling some stats from the grin engine to pull information 
 +  * The wall time is large 
 +  * A variant file with the bubble pop counted the contigs  
 +  * The group is planning on using the mate-pair data 
 +  * Do adapter removal and index removal - using skewer 
 +  *  ​
lecture_notes/05-15-2015.1431961376.txt.gz · Last modified: 2015/05/18 15:02 by gepoliano