weird problem with summit.bed file from macs2

Question

[mikysyc2016]

Hi all, I just find my bed file after using macs2 is not common(all the end - start equal to 1). But other files as narrow.peak and excel file are common. And bedgraph is also common( can see clear peak in IGV). summint.bed: chr1 3127206 3127207 ppar_2.72_peak_1 2.44687 chr1 3141438 3141439 ppar_2.72_peak_2 5.84966 chr1 3603620 3603621 ppar_2.72_peak_3 5.34279 ....... narrow peaks: chr1 3127019 3127287 ppar_ko1_2.72_peak_1 24 . 4.17374 5.25954 2.44687 187 chr1 3141408 3141611 ppar_ko1_2.72_peak_2 58 . 6.87514 10.28014 5.84966 30 chr1 3603509 3603773 ppar_ko1_2.72_peak_3 53 . 6.26061 9.49989 5.34279 111

this is the command i used: $ macs2 callpeak -t '/home//Desktop/FGC1867_s_4_CGATGT.bt2.sorted.bl.bam' -c '/home/Desktop/FGC1867_s_4_TTAGGC.bt2.sorted.bl.bam' -f BAM -g mm --bdg -n ppar_2.72 -q 0.01 --outdir ppar2_0.01_q

Can you give me some suggestion? Thanks a lot!

[mikysyc2016]

It is a summit bed, so i think it is the right type. And narrowpeak is a bed file not just give peak summit. I think that will be the reason. Is it right?

Answer 1

[jared.andrews07]

The summits file is just that - the summit of each peak. It's showing the position (base) for each peak that has the highest signal. That's what they're supposed to look like.