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Old 12-22-2014, 09:45 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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Originally Posted by westerman View Post
...I think that Brian's example will only produce two files -- one when *both* pairs pass the given parameters (in this case no-phiX, avg quality >= 10) and another file that contains pairs when *either* of the pairs fails.
That's true, though note that there is also a "reib" ("removeifeitherbad") flag which will switch the behavior between removing pairs if either fails, and removing only if both fail.

And it's also true that there's not much point in storing reads that fail quality metrics (unless you want to do some kind of QC analysis on them); it makes more sense when used for kmer filter.
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