I have an issue regarding to ChIP-seq analysis. Our combio did differential peak analysis to compare conditions A vs B.
When I uploaded the bidwig files I found that the gene of interest showed opposite results. From the differential peak analysis, the binding of X was upregulated, while the bigwig files showed it was obviously down (same scaling for A and B). Some genes were consistent though. Our combio did not give me an answer. Could anybody explain what caused such discrepancies?