run_stringtie: Run Stringtie

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run Stringtie

Description

Runs the stringtie tool

Usage

run_stringtie(
  input = NULL,
  threads = 10,
  trimming = TRUE,
  strandedness = NULL,
  reference.gtf = NULL,
  trans.estimate = FALSE,
  gene.estimate = FALSE,
  merge = FALSE,
  out = NULL,
  sample.name = NULL,
  ballgown = FALSE,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  stringtie = NULL,
  version = FALSE
)

Arguments

input	List of aligned files in sorted bam format, required
threads	Number of threads for stringtie to use, default set to 10
trimming	Disable trimming of predicted transcripts based on coverage, by default coverage trimming is enabled
strandedness	Strand spcific reads, values are "first" or "second"
reference.gtf	Path to the gtf file for guiding the assembly process
trans.estimate	Estimates the abundance of given reference transcripts, requires the reference GTF
gene.estimate	Estimates the abundance of given reference genes, requires the reference GTF
merge	Assemble transcripts from multiple input files generating a unified non-redundant set of isoforms
out	Name of the directory from the Kallisto output. If NULL, which is the default, a directory named "stringtie" is created in the current working directory.
sample.name	List of the sample names, required
ballgown	Enable output of Ballgown table files which will be created in the same directory as the output GTF (requires -G, -o recommended)
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
stringtie	Path to the stringtie program, required
version	Returns the version number

Value

A list with the stringtie commands

Examples

 ## Not run: 
# Version
stringtie.commands <- run_stringtie(stringtie = "/software/stringtie-1.3.6/stringtie",
                                    version = TRUE)
stringtie.commands

# Test command
sample_names <- unlist(lapply(strsplit(list.files(path = "trimmed_reads",
                       pattern = "*_R1_001.fastq$", full.names = FALSE),"_"), `[[`, 1))
gtf <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCh38_release_79/Sequence/Transcriptome/
         WholeTranscriptome/Homo_sapiens_GRCh38_79_primary_assembly_whole_transcriptome.gff"
bam.files <- list.files(path = hisat.alignments.dir, pattern = "sorted.bam$",
                        full.names = TRUE, recursive = TRUE)
stringtie.commands <- run_stringtie(input = bam.files,
                                    trimming = FALSE,
                                    strandedness = "first",
                                    reference.gtf = gtf,
                                    trans.estimate = TRUE,
                                    gene.estimate = TRUE,
                                    out = "stringtie",
                                    sample.name = sample_names,
                                    stringtie = "/software/stringtie-1.3.6/stringtie")
stringtie.commands

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.