I am new to bioinformatics and am doing it for the first time for my master's thesis. I've performed CUT&RUN between two conditions with H3K27ac and IgG as a control. I crosslinked the histone mod to DNA with PFA which is known to reduce signal.
Everything was looking fine between the two conditions, nothing strange during alignment (Bowtie2) or clean-up (remove MAPQ <10, chrM/Un/N), both conditions show very similar alignment rates, number of reads dropped, and size distributions. Even after peak calling (SEACR) the FRiP scores are very similar. However, the IGV tracks are almost completely peakless for one of the conditions, and correspondingly DiffBind showed 11 differential peaks in this condition and >5000 in the other.
What I can't seem to figure out is why the data processing doesn't give any indication of a failed experiment? Or does it, and I've just been looking in the wrong places?
Let me know if there is any relevant information missing. Thanks!