Question: MACS callpeak no summit location with --broad option
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gravatar for AlicePsyche
2.1 years ago by
AlicePsyche20
United Kingdom
AlicePsyche20 wrote:

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!

ADD COMMENTlink modified 2.1 years ago by genomax65k • written 2.1 years ago by AlicePsyche20

Try Homer pipeline at the link here.

ADD REPLYlink written 2.1 years ago by mks002160

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.

enter image description here

Figure example

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by AlicePsyche20

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 ....

ADD REPLYlink written 2.1 years ago by Lila M 470

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

ADD REPLYlink written 2.1 years ago by AlicePsyche20

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

ADD REPLYlink written 2.1 years ago by Lila M 470

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

ADD REPLYlink written 23 months ago by vps76710
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