Question: ChIPseeker result of covplot all over the place
gravatar for Stane
23 months ago by
Stane40 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 ?  



ADD COMMENTlink written 23 months ago by Stane40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 352 users visited in the last hour