ChIPseeker combining all files

Question

[Mo]

Hello Guys,

I did the following ways to get the annotation for each chip-seq data

1- Trim adaptors TrimGalore!
2- Aligned trimmed reads and sorts/converts to bam 
3- Mark duplicates and filter reads
4- Quality metrics 
5- Calculate cross-correlation 
6- Call peaks

then I annotate each sample with ChIPseeker, so the input was the one

The problem is that I have now 6 annotated files and when I combine them using gene symbols (which has few per each start and end) then it gets more complicated. for instance, I may not be able to match exact start and end together for comparison

I would like to know if you have any strategy to combine such files? or will you even combine them before you do annotation?

Let me know your thoughts Thanks