# DiffBind, diffferentially binding site

I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates.

when I run the diffBind package I have three contrast:

Silence1-Activation
Silence1-Silence2
Silence2-Activation


When I run dba.plotBox for any of contrasts I will have the same distribution of reads.like below: I even tried to start with 1000 peaks of each one that showed higher fold change but again got the same pattern for plotbox. How can I see which peaks belong to which histone marks?

• most likely the data frame is wrangled wrongly. Even the outliers are the same. This is almost impossible Jul 10 '20 at 12:40