Which parameter can be used to set up cutoff not to call peaks <150bp for the macs2 broad peak calling

Question

[lhaiyan3]

Dear all,

I don't want to call peaks <150bp in the macs2 broadpeak calling. Can you please tell me some suggestions which parameter I can use to set up the cutoff? Thanks very much.

best

HY

Answer 1

[ATpoint]

It is the --min-length parameter you are looking for. Was added to MACS last year and is not yet in the documentation on Github. If you call macs2 callpeak without further options you'll find

--min-length MINLEN   Minimum length of a peak. The DEFAULT value is the
                        predicted fragment size d. Note, if you set a value
                        smaller than the fragment size, it may have NO effect
                        on the result. For BROAD peak calling, try to set a
                        large value such as 500bps. You can also use
                        '--cutoff-analysis' option with default setting, and
                        check the column 'avelpeak' under different cutoff
                        values to decide a reasonable minlen value.

[lhaiyan3]

Great. Thanks very much for the information. It works!

[WouterDeCoster]

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