The starting point of a DESeq2 analysis is a count matrix K with one row for each gene i and one column for each sample j. The matrix entries Kij indicate the number of sequencing reads that have been unambiguously mapped to a gene in a sample. Note that although we refer in this paper to counts of reads in genes, the methods presented here can be applied as well to other kinds of HTS count data. For each gene, we fit a generalized linear model (GLM) [12] as follows.
