Stringtie

Transcript assembly and quantification for RNA-Seq

Citation

Citation: 10.1038/nbt.3122

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - stringtie

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

quant

Assemble transcripts and estimate their abundance from aligned reads (BAM)

Basic Usage:

result <- sn_run("stringtie", "quant",
  # Add your parameters here
)

merge

Merge assembled transcripts across multiple samples

Basic Usage:

result <- sn_run("stringtie", "merge",
  # Add your parameters here
)

Examples

Quant Example

library(ShennongTools)

result <- sn_run("stringtie", "quant",
  bam = "alignment.bam",
  gtf = "annotations.gtf",
  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")
}

Merge Example

library(ShennongTools)

result <- sn_run("stringtie", "merge",
  gtf_list = "example_file",
  merged_gtf = "annotations.gtf",
  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")
}

Parameters Reference

quant Parameters

Inputs:

Parameter	Type	Required	Description
`bam`	bam	Yes	Aligned reads in BAM format
`annotation`	gtf	No	Reference annotation to guide assembly

Outputs:

Parameter	Type	Required	Description
`gtf`	gtf	Yes	Output assembled transcripts in GTF format
`abundance`	tsv	No	Transcript abundance file (gene abundance or transcript TPMs)

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use
`extras`	string	“”	Additional arguments for StringTie

merge Parameters

Inputs:

Parameter	Type	Required	Description
`gtf_list`	tsv, txt	Yes	Text file listing multiple GTFs to be merged
`reference`	gtf	No	Optional reference annotation GTF

Outputs:

Parameter	Type	Required	Description
`merged_gtf`	gtf	Yes	Merged transcript annotations in GTF format

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use
`extras`	string	“”	Additional arguments for StringTie merge