Provided by: macs_3.0.1-2build1_amd64
NAME
macs3 - macs3 - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs3 [-h] [--version] {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac} ... macs3 -- Model-based Analysis for ChIP-Sequencing 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