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Old 02-28-2019, 07:27 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049

Sounds like bcl2fastq experienced a software issue. I suggest that you re-run the demultiplexing. I have seen this posted rarely and if I recall had experienced it one time. bcl2fastq re-run fixed the problem.

I will also put a plug in for from BBMap suite. It allows detection of all/optical dups without alignment of data.
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