Question: How to do the peak calling with "MACS2 bdgbroadcall" for H3K9me3 ChIP-seq
gravatar for b8921019
11 months ago by
b892101910 wrote:

Hi, I try to use the MACS2 bdgbroadcall to analyze my H3K9me3 ChIP-seq data, but there is no option for "ChIP-Seq Control File", like the MACS tool. How can I normalize my IP with the input while I do the peak calling? Because this is the first time to analyze the data by myself, is there any good workflow to follow?

chip-seq bdgbroadcall macs macs2 • 1.4k views
ADD COMMENTlink modified 11 months ago • written 11 months ago by b892101910
gravatar for b8921019
11 months ago by
b892101910 wrote:

Thanks for the instruction. Since I want to analyze broad marker, such as H3K9me3 and H3K27me3, should I change any parameter in the MACS2 callpeak to fit my study? If doing MACS2 callpeak can do the broad peak calling, what's the purpose of doing MACS2 bdgbroadcall after MACS2 callpeak? Because I originally intend to use SICER to do the peak calling, will it change the analysis result by using MACS2?


ADD COMMENTlink written 11 months ago by b892101910

MACS2 has a --broad option (this is the "Advanced Option" -> "Composite broad regions" -> "broad regions" option in Galaxy). I strongly encourage you not to directly run bdgbroadcall at any point, instead simply use MACS2 callpeak. The various bdg* programs are run internally by callpeak already. Their presence in Galaxy (and on the command line) is mostly to allow expert users to manually tweak and debug things, but I wouldn't suggest that anyone use them without a very compelling reason.

ADD REPLYlink written 11 months ago by Devon Ryan1.9k
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool is run on MACS2 callpeak output, so there is no need to input the control again.

Galaxy tutorials:

Also see the MACS2 manual, google group, and online discussion at sites like


ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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