run_kallisto: Run Kallisto

Description Usage Arguments Value Examples

View source: R/run_kallisto.R

Description

Runs the kallisto quant tool

Usage

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run_kallisto(
  mate1 = NULL,
  mate2 = 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,
  kallisto = "",
  version = FALSE
)

Arguments

mate1

List of the paths to files containing to the forward reads, required

mate2

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

kallisto

Path to the kallisto program, required

version

Returns the version number

Value

A list with the kallisto commands

Examples

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 ## 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(mate1 = mate1,
                              mate2 = 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(mate1 = 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 June 19, 2021, 1:08 p.m.