Different SEACR peak calling results between IgG and 2ndAbOnly (negative controls)

[jqiu1]

Hi all,

I called peaks using SEACR with IgG and 2nd antibody_only as negative controls. It works fine for other proteins of interest except for p300, and the SEACR results are not consistent.

When I used IgG as a negative control (norm, relaxed), much more peaks were called, but the max signal is very low. However, when I used 2ndAbOnly as a negative control (norm, relaxed), much less peaks were called, and the max signal is much higher (at least 10 fold). I am attaching the screenshots of SEACR output bed files for IgG, 2ndAbOnly in the email for the reference. I would appreciate if you could help with it.

Thank you in advance for your help!

Thanks,
Jingyun

[icanwinwyz]

Hi Jingyun,
I got a similar issue as yours. What library size for your samples and two negative controls?