I used MACS2 to call differential peaks. I got the results but there was a problem bothering me much. The final result missed some important peaks. For example, gene A is a marker gene for cell type A. I have seen the peaks (fold enrichment: 3-4; the peak length 200-1200) in the peak file from cell type A after broad peak calling by MACS2, which were absent in the peaks file from cell type B. However, after call differential binding events for cell type A and B, those peaks were not in the final results. I have tried used different parameters to call differential binding events, like -g 60 or 100 or 200. But the problem was still unsolved. Any ideas?
Here is my script: macs2 bdgdiff --t1 A_treat_pileup.bdg --c1 A_control_lambda.bdg --t2 B_treat_pileup.bdg --c2 B_control_lambda.bdg --d1 17119467 --d2 17119467 -g 60 -l 120 --o-prefix diff_A_vs_B
Duplicate of previous post.