positional arguments:

{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}

callpeak

Main MACS3 Function: Call peaks from alignment results.

bdgpeakcall

Call peaks from bedGraph file.

bdgbroadcall

Call nested broad peaks from bedGraph file.

bdgcmp

Comparing two signal tracks in bedGraph format.

bdgopt

Operate the score column of bedGraph file.

cmbreps

Combine bedGraph files of scores from replicates.

bdgdiff

Differential peak detection based on paired four bedGraph files.

filterdup

Remove duplicate reads, then save in BED/BEDPE format file.

predictd

Predict d or fragment size from alignment results. In case of PE data, report the average insertion/fragment size from all pairs.

pileup

Pileup aligned reads (single-end) or fragments (paired-end).

randsample

Randomly choose a number/percentage of total reads, then save in BED/BEDPE format file.

refinepeak

Take raw reads alignment, refine peak summits. Inspired by SPP.

callvar

Call variants in given peak regions from the alignment BAM files.

hmmratac

Dedicated peak calling based on Hidden Markov Model for ATAC-seq data.

options:

-h, --help

show this help message and exit

--version

show program's version number and exit

For command line options of each command, type: macs3 COMMAND -h