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Old 02-28-2019, 07:21 AM   #1
ECO
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Default Exact duplicate reads/readnames/quality/tiles in Novaseq FASTQs

Anyone seen this? Some (not correlated with software versions AFAICT) of our MarkDuplicates jobs are failing because there are exact copies of the same reads in the fastq. Identical readnames, locations/tiles, sequence, qualities.

Really weird...
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Old 02-28-2019, 07:27 AM   #2
GenoMax
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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 clumpify.sh from BBMap suite. It allows detection of all/optical dups without alignment of data.
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Old 02-28-2019, 11:07 AM   #3
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We've run it several times to no effect, but are re-running it now with single threaded writing...I'm hopeful that helps....
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Old 02-28-2019, 02:25 PM   #4
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Interesting. Let us know what happens.
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