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