Question: tag count and fold enrichment
gravatar for mikysyc2016
14 months ago by
mikysyc201650 wrote:

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!

chip-seq • 530 views
ADD COMMENTlink modified 14 months ago by ATpoint21k • written 14 months ago by mikysyc201650
gravatar for ATpoint
14 months ago by
ATpoint21k wrote:

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 ╬╗local 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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by ATpoint21k
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