Macs2

Model-based Analysis of ChIP-Seq (MACS2) for peak calling

Citation

Citation: 10.1186/gb-2008-9-9-r137

Environment

This tool uses the following conda environment:

Channels: - bioconda - conda-forge

Dependencies: - macs2

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("macs2", "callpeak", ...)

Available Commands

callpeak

Call peaks from aligned ChIP-seq reads

Basic Usage:

result <- sn_run("macs2", "callpeak",
  # Add your parameters here
)

bdgcmp

Compare treatment and control signal tracks (e.g., FE, logLR)

Basic Usage:

result <- sn_run("macs2", "bdgcmp",
  # Add your parameters here
)

Examples

Callpeak Example

library(ShennongTools)

result <- sn_run("macs2", "callpeak",
  treatment = "alignment.bam",
  peaks = "example_file",
  threads = 1,
  format = "BAM"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Bdgcmp Example

library(ShennongTools)

result <- sn_run("macs2", "bdgcmp",
  tfile = "input_file.txt",
  cfile = "input_file.txt",
  outfile = "input_file.txt"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

callpeak Parameters

Inputs:

Parameter	Type	Required	Description
`treatment`	bam	Yes	Aligned reads from ChIP-seq experiment
`control`	bam	No	Control/input sample (optional)

Outputs:

Parameter	Type	Required	Description
`peaks`	narrowPeak, broadPeak	Yes	Peak calling result files
`summits`	bed	No	Summits of peaks (optional)
`log`	txt	No	Log file with command summary

Parameters:

Parameter	Type	Default	Description
`format`	string	“BAM”	Format of input files (e.g., BAM, BED, ELAND)
`genome_size`	string	“hs”	Effective genome size (e.g., hs, mm, ce, dm)
`name`	string	“macs2_output”	Prefix name for output files
`qvalue`	numeric	0.05	FDR cutoff for peak detection
`broad`	boolean	FALSE	Enable broad peak calling
`threads`	integer	1	Number of threads (for future parallel extensions)
`extras`	string	“”	Additional arguments to pass to MACS2

bdgcmp Parameters

Inputs:

Parameter	Type	Required	Description
`tfile`	bedgraph	Yes	Treatment bedGraph file (e.g., *_treat_pileup.bdg)
`cfile`	bedgraph	Yes	Control bedGraph file (e.g., *_control_lambda.bdg)

Outputs:

Parameter	Type	Required	Description
`outfile`	bedgraph	Yes	Output comparison signal track

Parameters:

Parameter	Type	Default	Description
`method`	string	“FE”	Comparison method (FE, logLR, ppois, qpois)
`pseudocount`	numeric	1	Pseudocount added to avoid division by zero
`extras`	string	“”	Extra parameters for bdgcmp