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:
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!