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MACS2 bdgbroadcall (version 2.2.9.1+galaxy0)

bedGraph generated MACS:

Cutoff for peaks:

Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)

Cutoff for peaks:

Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. Default=1 (--cutoff-link)

Minimum length of peak:

It is recommended to set it as d value. Default=200 (--min-length)

Maximum gap between significant peaks:

It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)

Maximum linking between significant peaks:

It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)

What it does

This is bdgbroadcall utility from the MACS2 Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.

Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.