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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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phiX filtering? #10

Closed gregcaporaso closed 8 years ago

gregcaporaso commented 8 years ago

@benjjneb, does the DADA2 script in this repo perform phiX filtering? I'm working on some test data, and seeing a lot of phiX in my data set after DADA2.

benjjneb commented 8 years ago

Not as currently written. It can be added to the fastqFilter call though, eg:

fastqFilter(unfilts[i], filteredFastq, truncLen=truncLen, trimLeft=trimLeft, rm.phix=TRUE)
gregcaporaso commented 8 years ago

Thanks, I'll try this out!