Q: There's a huge difference between my peak number and the bio company's peak number

[bigshark12345]

When I use macs3 call peak(for atac), I only get 5500 peaks, But when I checked the bio company's report, they got a peak of 30,000.
I want to know the possible reasons。
Here's my code：
macs3 callpeak -g 762311306 -t MF-1-A.final.bam --name ./MF1A -B --format BAM --qvalue 0.075 --cutoff-analysis --broad --nomodel --shift -75 --extsize 150

[taoliu]

@bigshark12345 Did the bio company use the same parameters as those in your command? By the way, I would suggest you not using --broad for ATAC-seq data analysis. The peaks in ATAC-seq is not supposed to be 'broad' as some histone marks for which the 'broad mode' was designed for.

[bigshark12345]

@taoliu ，I tried the exact same parameters last week and got a peak of 9000, but it's still a big difference from what they reported. I looked back at the previous analysis, like inserting the fragment distribution map, and it didn't look very healthy data either。--broad should be delete?