I need to do differential ChIP-Seq analysis to find the binding of genes between 2 conditions. I know there are lots of tools for that but I decided to use DESeq2 for that. I used MACS for peak calling and I had BAM files. Then used featureCounts to generate counts matrix. To this count matrix, I used DESeq2.
Everything looks fine but I am not sure is this method sensible or not but I needed differential analysis with gene names. Can I do this without a doubt?