I am dooing atac seq data analysis so far what i have done
- I aligned the data with bowtie2
- Removed duplicates
- made bed files out of those bed file
- Did peak calling with Homer using it findPeak command -Now i have list of peak files with respect to various condition . In Homer manual i read a function called findMotifsgenome function , i have some confusion here how do i proceed from here do i have to just give the peak file as it is or I have to process the peak files .
Any suggestion or help would be highly appreciated