Hi. I would like to perform differential peak analysis for my CUT&Tag data. I converted the bam files of the samples to bedgraph files. I then normalized the signal of the bedbraph files using a normalization factor calculated based on the E. coli bacterial read count. Since my Tn5 enzyme was extracted in E coli, the bacterial read count can therefore serve as an internal spike in control. I then use SEACR, which is the recommended peak caller for CUT&Tag experiments to call peaks for my samples.
For the next step I would like to perform differential peak analysis using Diffbind. But my question is how to normalize the samples using pre-calculated normalizing factor? In the Reference Manual it mentioned that users can supply normalization factors by using the DBA_NORM_USER command, how exactly this can be done?
For example, I have 6 samples in 2 groups, with the following normalization factor : Group 1: 0.85, 0.96, 1.2,
Group 2: 1.1, 0.9, 0.8