I know DESeq2 expects raw read counts as the inputs which is important for DESeq2's statistical model to hold (it has been emphasized many many times).
For singed-end reads, the counts should be the number of reads mapped to the gene. But, how about paired-end data, is it the number of mapped reads or fragments to the gene?
In another word, do I need to multiple 2 for the counts from htseq-count for PE data because htseq-count count reads pairs for PE data?
Thank you so much!