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