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Old 07-04-2015, 05:40 AM   #2
Michael Love
Senior Member
Location: Boston

Join Date: Jul 2013
Posts: 333

For DESeq2, you shouldn't use any kind of values where the library size has been divided out. The statistical methods use the properties of the sampling distribution of counts, as well as estimation of additional variation (dispersion), for inference.

The input matrix should be: the number of reads/fragments which can be uniquely assigned to a gene (aligning to any of the exons of a gene).
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