Deeptools

A suite of tools to process and visualize deep sequencing data

Citation

Citation: 10.1093/nar/gkw257

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - deeptools

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

bamcoverage

Generate normalized bigWig files from BAM files

Basic Usage:

result <- sn_run("deeptools", "bamcoverage",
  # Add your parameters here
)

computematrix

Compute scores over genomic regions for heatmap/profile plots

Basic Usage:

result <- sn_run("deeptools", "computematrix",
  # Add your parameters here
)

plotheatmap

Plot a heatmap from a computeMatrix output

Basic Usage:

result <- sn_run("deeptools", "plotheatmap",
  # Add your parameters here
)

plotprofile

Plot an average profile from a computeMatrix output

Basic Usage:

result <- sn_run("deeptools", "plotprofile",
  # Add your parameters here
)

Examples

Bamcoverage Example

library(ShennongTools)

result <- sn_run("deeptools", "bamcoverage",
  bam = "alignment.bam",
  bigwig = "example_file",
  threads = 4
)

# 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")
}

Computematrix Example

library(ShennongTools)

result <- sn_run("deeptools", "computematrix",
  bigwig = "example_file",
  regions = "regions.bed",
  matrix = "example_file",
  threads = 4
)

# 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")
}

Plotheatmap Example

library(ShennongTools)

result <- sn_run("deeptools", "plotheatmap",
  matrix = "example_file",
  heatmap = "example_file"
)

# 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")
}

Plotprofile Example

library(ShennongTools)

result <- sn_run("deeptools", "plotprofile",
  matrix = "example_file",
  profile = "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

bamcoverage Parameters

Inputs:

Parameter	Type	Required	Description
`bam`	bam	Yes	Input BAM file

Outputs:

Parameter	Type	Required	Description
`bigwig`	bigwig	Yes	Output bigWig file

Parameters:

Parameter	Type	Default	Description
`bin_size`	integer	50	Bin size for coverage computation
`normalization`	string	“RPKM”	Normalization method (e.g., RPKM, CPM, BPM, RPGC, None)
`threads`	integer	4	Number of threads to use
`extras`	string	“”	Additional options to pass to bamCoverage

computematrix Parameters

Inputs:

Parameter	Type	Required	Description
`bigwig`	bigwig	Yes	Input bigWig file
`regions`	bed	Yes	BED/GTF file with regions of interest

Outputs:

Parameter	Type	Required	Description
`matrix`	tsv	Yes	Output matrix file

Parameters:

Parameter	Type	Default	Description
`mode`	string	“reference-point”	Mode of matrix computation: reference-point or scale-regions
`reference_point`	string	“TSS”	Reference point if using reference-point mode
`before`	integer	1000	Distance upstream of the reference point
`after`	integer	1000	Distance downstream of the reference point
`threads`	integer	4	Number of threads
`extras`	string	“”	Additional options

plotheatmap Parameters

Inputs:

Parameter	Type	Required	Description
`matrix`	tsv	Yes	Input matrix from computeMatrix

Outputs:

Parameter	Type	Required	Description
`heatmap`	png	Yes	Output heatmap image

Parameters:

Parameter	Type	Default	Description
`color_map`	string	“RdBu”	Colormap name
`extras`	string	“”	Additional arguments

plotprofile Parameters

Inputs:

Parameter	Type	Required	Description
`matrix`	tsv	Yes	Input matrix from computeMatrix

Outputs:

Parameter	Type	Required	Description
`profile`	png	Yes	Output profile plot image

Parameters:

Parameter	Type	Default	Description
`per_group`	boolean	FALSE	Plot individual group profiles
`extras`	string	“”	Additional arguments