Question: Which parameter can be used to set up cutoff not to call peaks <150bp for the macs2 broad peak calling
1
gravatar for lhaiyan3
12 weeks ago by
lhaiyan330
United States
lhaiyan330 wrote:

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

chip-seq macs2 • 179 views
ADD COMMENTlink modified 12 weeks ago by ATpoint18k • written 12 weeks ago by lhaiyan330
2
gravatar for ATpoint
12 weeks ago by
ATpoint18k
Germany
ATpoint18k wrote:

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.
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by ATpoint18k

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

ADD REPLYlink written 12 weeks ago by lhaiyan330

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
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ADD REPLYlink written 12 weeks ago by WouterDeCoster39k
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