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)
- 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?
- From the homer file:
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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!
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written
by
mikysyc2016
1 answer
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.
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