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