MACS callpeak no summit location with --broad option
0
0
Entering edit mode
5.5 years ago
AlicePsyche ▴ 30

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!

ChIP-Seq software error sequencing • 3.0k views
ADD COMMENT
0
Entering edit mode

Try Homer pipeline at the link here.

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2282 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6