Adding a shift with MACS3

[nleroy917]

I'm comparing macs3 peak calling procudures around various forums and code bases. I started here: https://github.com/macs3-project/MACS/discussions/435 on the macs3 repo.

It references a tweet where people regularly mention adding a --shift 100 argument to the macs3 call. I'm curious if this is done here or not? It seems that the use of the --shift parameter in macs3 is primarily to adjust the positioning of the reads before peak calling, which is particularly important for ATAC-seq data due to how the cutting sites are represented.

It seems like not when I look at the code:

cmd_base = [
        "{} callpeak".format(tools.macs3),
        ("-t", peak_input_file),
        ("-f", "BED"),
        ("--outdir", peak_folder),
        ("-n", args.sample_name),
        ("-g", args.genome_size)
]

[nleroy917]

Nevermind, I think I see it in the config file.

  macs3:
    params: '--shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01'

[nleroy917]

Ok I think I answered myself, so I will close