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Old 08-10-2017, 07:26 AM   #4
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Location: Washington, D.C. metro area

Join Date: Feb 2010
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Technically, yes, but whether you would want to do so will depend partially on your coverage needs and your tolerance for sequencing errors.

Using paired end reads of 300bp from either end will cover the amplicon with about 70bp of overlap in the middle, but reads in only one direction covering ~230bp on either side of that. You may not have a lot of coverage on the amplicon ends to indicate whether a detected variant is real or an error. Whether that would be a problem for you will depend, at least partly, on the design of your experiment.
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