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Old 10-16-2015, 09:55 AM   #5
thermophile
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Location: CT

Join Date: Apr 2015
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The base quality will be significantly improved if you fully overlap your reads for amplicon sequencing. see http://aem.asm.org/content/79/17/511...7-5d313d15b9a5 for a comparison of the sequence quality for different lenghts of 16s sequencing.

If you're interested in very small number of base differences, you absolutely need to fully overlap. If you need 5-10% differences, maybe you could get away with not fully overlapping. But the cost difference between the 2 kits is only a couple of hundred $, your downstream computation time will be much much greater with marginal sequences which likely will cost thousands rather than hundreds

ETA-my cost estimate for computational time is based on 16S, I've never dealt with any of the cancer panels so don't know how significantly poor quality bases would impact your results

Last edited by thermophile; 10-16-2015 at 09:57 AM.
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