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Old 05-08-2015, 01:16 PM   #14
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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I finally finished downloading these, and I'll take a look at the quality from mapping. But before I do that, I always trim adapters... but I was never sure what kind of adapters PhiX reads had. They don't exactly match any adapters in my list, so I'll call them "PhiX adapters". Here they are, for reference:

>Read1_adapter
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAA
>Read2_adapter
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA

Also, at least for the first 4 million reads, 29.36% failed the chastity filter.
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