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Old 05-18-2017, 12:16 PM   #229
Brian Bushnell
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Location: Walnut Creek, CA

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Probably the one trimming more is better. Geneious is probably trimming more by overlap because overlap trimming happens after adapter-sequence trimming, so if some adapter sequences are missing, those will (usually) get overlap-trimmed rather than sequence-trimmed. But it's hard to say. You could align the first 1m reads to the reference (if you have one) and look at the mapping rates and error rates to see which dataset is better.
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