Star

Spliced Transcripts Alignment to a Reference (STAR)

Citation

Citation: 10.1093/bioinformatics/bts635

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - star

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

index

Generate genome index for STAR

Basic Usage:

result <- sn_run("star", "index",
  # Add your parameters here
)

align

Align RNA-seq reads to the reference genome using STAR

Basic Usage:

result <- sn_run("star", "align",
  # Add your parameters here
)

solo

Perform single-cell RNA-seq alignment and quantification using STARsolo

Basic Usage:

result <- sn_run("star", "solo",
  # Add your parameters here
)

Examples

Index Example

library(ShennongTools)

result <- sn_run("star", "index",
  fasta = "sequences.fasta",
  genome_dir = "reference.fasta",
  threads = 8
)

# 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")
}

Align Example

library(ShennongTools)

result <- sn_run("star", "align",
  genome_dir = "reference.fasta",
  read1 = "sample_R1.fastq.gz",
  bam = "alignment.bam",
  threads = 8
)

# 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")
}

Solo Example

library(ShennongTools)

result <- sn_run("star", "solo",
  genome_dir = "reference.fasta",
  read1 = "sample_R1.fastq.gz",
  read2 = "sample_R2.fastq.gz",
  solo_output = "output_file.txt",
  threads = 8
)

# 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

index Parameters

Inputs:

Parameter	Type	Required	Description
`fasta`	fasta	Yes	Reference genome in FASTA format
`gtf`	gtf	No	Gene annotation in GTF format

Outputs:

Parameter	Type	Required	Description
`genome_dir`	directory	Yes	Output directory for STAR genome index

Parameters:

Parameter	Type	Default	Description
`threads`	integer	8	Number of threads to use
`sjdbOverhang`	integer	100	Read length - 1 for spliced junction detection
`extras`	string	“”	Additional STAR arguments

align Parameters

Inputs:

Parameter	Type	Required	Description
`genome_dir`	directory	Yes	STAR genome index directory
`read1`	fastq	Yes	First read FASTQ file
`read2`	fastq	No	Second read FASTQ file (optional for single-end)

Outputs:

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

Parameters:

Parameter	Type	Default	Description
`threads`	integer	8	Number of threads
`output_prefix`	string	“star_”	Prefix for output files
`outSAMtype`	string	“BAM SortedByCoordinate”	BAM output type
`extras`	string	“”	Extra STAR options

solo Parameters

Inputs:

Parameter	Type	Required	Description
`genome_dir`	directory	Yes	STAR genome index directory
`read1`	fastq	Yes	Read 1 FASTQ file (usually cell barcode + UMI)
`read2`	fastq	Yes	Read 2 FASTQ file (RNA read)
`whitelist`	txt	No	Cell barcode whitelist (e.g. 10x barcodes)

Outputs:

Parameter	Type	Required	Description
`solo_output`	directory	Yes	Output directory for STARsolo quantification results

Parameters:

Parameter	Type	Default	Description
`threads`	integer	8	Number of threads
`solo_type`	string	“CB_UMI_Simple”	Type of single-cell protocol
`solo_features`	string	“Gene”	Features to quantify (e.g., Gene, GeneFull, SJ)
`solo_cell_filter`	string	“EmptyDrops_CR”	Cell calling method
`output_prefix`	string	“starsolo_”	Output file prefix
`extras`	string	“”	Additional STARsolo options