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Old 08-14-2013, 07:33 AM   #4
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Well, as long as you have both platforms in both conditions, this is fine. Just treat the library type as a covariate, as in the example in the vignette. (There, we used on purpose a dataset with such a mixture of single-end and paired-end data to demonstrate how to use covariates.)
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