Hi
I would like to ask when I do compute matrix of my chipseq data in c elegans, I use Bamcoverage to normalise ChIPseq to input and get the signal ratio vs input (my bin size was set to 50).
Then, I used the Bigwig file generated from Bamcoverage to plot against the all genes gtf file with computematrix: Bin size = 10 , TSS as reference point ±2000bp, I saw a very sharp peak at TSS with Plotprofile.
Then, I also use Computematrix to plot Scale region (–regionBodyLength =2000) -a 2000 -b 2000 then I tried bin size of 1, 5, 50 all gives me a plot a massive board peak behind TSS that spread until TES and the TSS peak is much less obvious.
It is so confusing whether my protein bind TSS sharply or just cover whole gene region from TSS to TES, anyone could tell me what cause such issue?
