Differential ChIP-seq peaks and IGV
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?
Thanks.
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jun.yang2 •
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It is impossible to answer this from remote without any details. Please have a meeting with the analyst and discuss your issues.