search

FrietzeLabUVM / peaksat

R package to do peak saturation analysis for ChIP-seq.
1 stars 1 forks source link

broad option #1

Open WardDeb opened 1 week ago

WardDeb commented 1 week ago

Hi,

Thanks for the package, it's quite nice ! Is there an option to set peak calling to broad ?

Cheers,

WardDeb

jrboyd commented 1 week ago

Hi WardDeb, This not directly supported, but there are a couple ways you could accomplish what you want.

One would be to edit the script file that peaksat uses to run macs2. You can locate the script file from R easily with: system.file(package = "peaksat", "extdata/run_subsample_peak.sh", mustWork = TRUE)

There are 2 lines in that file that define macs2 commands and you'll need to edit both of them. Search for "callpeak" to locate them and add the --broad flag there. You can add any other broad peak related parameters you want too.

Note that if you reinstall peaksat or update you'll lose these changes.

You could also clone/fork peaksat if you're comfortable with git and installing R packages; then make these same changes for a more robust solution.

Keep in mind that beyond saturation the peak number will start going down as nearby peaks get merged together more and more. This happens with narrowPeak already but I expect will be more severe with broadPeak. You may want to consider looking at peak widths instead with peaksat::load_widths.

I'm glad you find the package useful, -Joe