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Old 10-17-2011, 09:02 AM   #7
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,541
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Hi Semyon

Could you clarify if the unaligned reads in SAM/BAM format from Illumina CASAVA 1.8.x have FLAG bit 0x200 (not passing quality controls) set according to your non-PF QC?

Thanks,

Peter
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