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Old 01-17-2018, 07:09 PM   #18
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Location: Melbourne

Join Date: Jan 2013
Posts: 1,121

Unknown reads source in indexed sequencing:

1- PhiX
2- indices that does not match those in sample sheet caused by base mis-match in excess of set numbers in bcl2 fastq. This is result of poor sequence quality due to over clustering or adapter/primer quality

Unknown reads are high when using desalted primers for amplicon libraries
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