run_kallisto: Run Kallisto

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

Run Kallisto

Description

Runs the kallisto quant tool

Usage

run_kallisto(
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  sample.name = NULL,
  fusion = NULL,
  strandedness = NULL,
  out.dir = NULL,
  threads = 10,
  bootstrap = 100,
  fragment.length = 300,
  std.dev = 25,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  kallisto = "",
  version = FALSE
)

Arguments

input1	List of the paths to files containing to the forward reads, required
input2	List of the paths to files containing to the reverse reads, required for paired end sequence data
index	Path to the reference transcriptome kallisto index, required
sample.name	List of the sample names, required
fusion	Search for fusions used for Pizzly
strandedness	Strand spcific reads, values are "first" or "second"
out.dir	Name of the directory from the Kallisto output. If NULL, which is the default, a directory named "kallisto" is created in the current working directory.
threads	Number of threads for kallisto to use, default set to 10
bootstrap	Number of bootstrap samples, default set to 100
fragment.length	Estimated average insert fragment size, must be set for single end sequence data
std.dev	Estimated standard deviation of insert fragment size, must be set for single end sequence data
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
kallisto	Path to the kallisto program, required
version	Returns the version number

Value

A list with the kallisto commands

Examples

 ## Not run: 
trimmed_reads_dir <- "trimmed_reads"
mate1 <- list.files(path = trimmed_reads_dir, pattern = "*_R1_001.fastq$", full.names = TRUE)
mate2 <- list.files(path = trimmed_reads_dir, pattern = "*_R2_001.fastq$", full.names = TRUE)

sample_names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
                       pattern = "*_R1_001.fastq$",
                       full.names = FALSE),"_"), `[[`, 1))

index <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCH38_p7/Sequence/Transcriptome/
          KallistoIndex/GRCh38_p7.kall"

strandedness <- "second"

# Paired end
kallisto.cmds <- run_kallisto(input1 = mate1,
                              input2 = mate2,
                              index = transcriptome,
                              sample.name = sample.names,
                              strandedness = strandedness,
                              out.dir = kalisto.results.dir,
                              kallisto = "/software/kallisto_v0.45.1/kallisto")
# Single end
kallisto.cmds <- run_kallisto(input1 = mate1,
                              index = transcriptome,
                              sample.name = sample.names,
                              strandedness = strandedness,
                              fragment.length = 300,
                              std.dev = 25,
                              out.dir = kalisto.results.dir,
                              kallisto = "/software/kallisto_v0.45.1/kallisto")

## End(Not run)

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