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Old 10-15-2015, 09:45 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

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You don't need a full overlap for amplicon libraries. You just need enough of an overlap to merge the reads. Depending on your read quality, a aiming for 30-50bp overlap should be fine.

Chimeric non-overlapping amplicons are hard to detect. If you cluster your pairs, and then find pairs in which the two reads map to different clusters, then you could assume that those pairs are chimeric. But the sensitivity and specificity depend completely on the quality of clustering.
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