tag count and fold enrichment

Question

[mikysyc2016]

Hi, When use masc2 to do peak calling will get a excel file which include fold enrichment( compare to input group). When use homer, it has one step to give you a file which include normalized tag count and control tags.(HOMER to count tags in each peak)

1. whether we still need to know tag count, if we know fold enrichment and FDR? what is the function of tag count for ChIP-seq analysis?
2. From the homer file:

.

Peak1 normalized tag count : 147.6  control tags : 37.1
Fold Change vs Control: 8.92      Fold Change vs Local : 16.48

I do not understand why fold change not equal to 147.6/37.1 close to 4? Thanks!

Answer 1

[ATpoint]

Because this macs fold change or fold enrichment, according to the paper is:

Candidate peaks with p-values below a user-defined threshold p-value (default 10-5) are called, and the ratio between the ChIP-Seq tag count and λlocal is reported as the fold_enrichment.

What this means in detail, I never figured out. That is why I only use the MACS peaks as template to aggregate reads, and then proceed with other tools like DESeq2 for downstream analysis.