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?
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?
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.
This tool is run on MACS2 callpeak output, so there is no need to input the control again.
Galaxy tutorials: https://galaxyproject.org/learn/
Also see the MACS2 manual, google group, and online discussion at sites like https://www.biostars.org/.