Subread

A ultrafast and accurate read summarization program

Citation

Citation: 10.1093/bioinformatics/btt656

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - subread

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

featurecounts

Count reads mapped to genomic features

Basic Usage:

result <- sn_run("subread", "featurecounts",
  # Add your parameters here
)

buildindex

Build Subread index from reference genome

Basic Usage:

result <- sn_run("subread", "buildindex",
  # Add your parameters here
)

Examples

Featurecounts Example

library(ShennongTools)

result <- sn_run("subread", "featurecounts",
  bam_files = "input_file.txt",
  annotation = "annotations.gtf",
  counts = "results.txt",
  threads = 1
)

# 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")
}

Buildindex Example

library(ShennongTools)

result <- sn_run("subread", "buildindex",
  fasta = "sequences.fasta",
  index = "genome_index"
)

# 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

featurecounts Parameters

Inputs:

Parameter	Type	Required	Description
`bam_files`	bam, sam	Yes	Input BAM/SAM files for read counting (space-separated if multiple)
`annotation`	gtf, gff	Yes	Annotation file in GTF/GFF format

Outputs:

Parameter	Type	Required	Description
`counts`	txt	Yes	Output count matrix file

Parameters:

Parameter	Type	Default	Description
`feature_type`	string	“exon”	Feature type in GTF annotation
`attribute_type`	string	“gene_id”	Attribute type in GTF annotation
`stranded`	integer	0	Strand-specific read counting (0: unstranded, 1: stranded, 2: reversely stranded)
`paired`	boolean	TRUE	Treat input as paired-end reads
`threads`	integer	1	Number of threads to use

buildindex Parameters

Inputs:

Parameter	Type	Required	Description
`fasta`	fasta	Yes	Input reference genome FASTA file

Outputs:

Parameter	Type	Required	Description
`index`	prefix	Yes	Output index prefix