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Old 05-08-2015, 09:12 AM   #4
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Originally Posted by DNATECH View Post
Thanks! Currently there are no local duplicate metrics in the SAV viewer and no options in bcl2fastq for flagging or filtering for these cases.
People working with X Ten data get their data already aligned and might be able to use picard etc.? However the HiSeq 3000/4000 will be used for all kinds of applications were alignment based analyses are not an option.
There are tools to address duplicates (e.g. from BBMap) but they are not cluster location/adjacency aware. Picard should be in this category too unless it has been modified.

I was wondering if this would be something illumina should implement in bcl2fastq software, specially if duplicates will be a problem with less than perfect libraries.
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