run_stringtie: Run Stringtie

Description Usage Arguments Value Examples

View source: R/run_stringtie.R

Description

Runs the stringtie tool

Usage

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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,
  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)

stringtie

Path to the stringtie program, required

version

Returns the version number

Value

A list with the stringtie commands

Examples

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 ## 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 March 26, 2021, 5:40 p.m.