MACS callpeak no summit location with --broad option

Question

[AlicePsyche]

Hi,

Is there a specific option to set when run macs2 in broad mode in order to get summit location? I want to call broad peaks for histone modification, when I run the following command:

macs2 callpeak -t my_sample.bed -n name -g 1.4e9 --broad --broad-cutoff 0.05 --nomodel --nolambda

The output files don't have NAME_summits.bed and there is no column of "absolute peak summit position". Did I use macs2 in wrong way?

Thanks for your help!

[mks002]

Try Homer pipeline at the link here.

[AlicePsyche]

Thanks for your reply! Actually I use Homer a lot, the only "problem" is that I want the summits location of the called peaks. For downstream analysis, it would be a lot easier to plot heatmap around the summit position(+/- 3K). I used to plot heatmap around peaks center but it looked a little funny as the most enriched signals were not aligned straightly.

Figure example

Is there a easy way to identify the summits location of the peaks Homer called?

[Lila M]

You don't have control file. Maybe you need one to use the callpeak option macs2 callpeak -t ChIP.bam -c Control.bam -n name -g 1.4e9 --broad --broad-cutoff 0.05 ....

[AlicePsyche]

I think macs2 is able to call peaks without control file?

[Lila M]

Maybe you can, but I always use a control file and I don't have any problem in get the summits file. Good luck!

[vps767]

Try something like macs2 refinepeak -i my_sample.bed -b name_peaks.broadPeak -f BED -o name_summits.bed