Question: ChIPseeker result of covplot all over the place
gravatar for Stane
12 months ago by
Stane30 wrote:


I have been trying to analyze a chip-seq sample from GEO and I don't understand the ouput of covplot function, I have full black bar on almost all chromosomes, is it the result of byproduct from the immunoprecipitation ? the bed file is also missing score values, could it be the problem ?

My second concern is that the chipset is targeting a protein that I found downregulated on all microarray with the same treatment and cell type. Is it possible to confirm that with ChipSeeker ? or should I re-run macs2 using the Control vs Treatment instead of Treatment vs Control to see If I get peaks at the location of the protein ?  



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