Would you like to tell me whether DESeq2 can analyze m6A-seq to detect differential m6A peaks? Other papers firstly used input reads to normalize m6A-seq reads, and then performed fisher’s exact test. It seems that DESeq2 can not accept normalized reads.
In DESeq2 instead of pre-scaling counts, you would just include the assay type as a design variable. Then you are essentially doing a paired analysis with assay type as the condition effect. E.g. ~sample + assay will compare, within each sample, the enriched vs input LFC. I would look at MA plots though as a diagnostic, and consider if you have features could be used to define controlGenes, but we don't have any automated workflows to do this. See ?estimateSizeFactors for description of controlGenes, and this step can then be run before DESeq if you want to specify that certain features be used for estimating the size factors.