Fold-change values in THOR differential peaks and post-processed bigwigs

[dmitrymyl]

Hi!

I call differentially enriched regions between two conditions: 1 ChIP sample per each and 1 Input sample per each. Besides p-values, I would like to obtain fold-change values between two conditions. I found that the 11th column of the output BED file contains counts for each condition.

1. What are these counts?
   1. Are these counts from original BAM files? If so, I can't use them for fold-changes.
   2. Are these counts from post-processed data? Are they obtained after TMM normalization between two ChIP samples or also after Input subtraction? If it's after TMM and Input subtraction, I could use them to estimate fold-changes.
2. Which values are stored in post-processed bigwigs for ChIP samples? Are they only after TMM normalization between two ChIP samples or also after Input subtraction? If it is the former, how can I obtain tracks after TMM + Input subtraction?

Thanks in advance!