run_mageck: Run Mageck

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

Run Mageck

Description

Run Mageck

Usage

run_mageck(
  command = NULL,
  umi.list = NULL,
  fastq = NULL,
  sample.label = NULL,
  prefix = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  version = NULL,
  mageck = NULL
)

Arguments

command	Mageck command to run, currently only count is implemented
umi.list	file contating the list of UMIs
fastq	Trimmed sample files in fastq format, should only contain the umi sequence after trimming with cutadapt
sample.label	Sample name
prefix	Name to add to results files
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
version	Returns the version number
mageck	Pathe to the mageck program, required

Value

List of Mageck commands

Examples

## Not run: 
path <- "/software/anaconda3/bin/mageck"

mageck.version <- run_mageck(version = TRUE,
                            mageck = path)
mageck.version

command <- "count"
list <- "umi-list.tsv"
reads <- "MPRA_R1.fastq.gz"
label <- "MPRA"
prefix <- "MPRA"

mageck.cmds <- run_mageck(command = command,
                          umi.list = list,
                          fastq = reads,
                          sample.label = label,
                          prefix = prefix,
                          execute = FALSE,
                          mageck = path)

mageck.cmds


## End(Not run)

GrahamHamilton/pipelineTools documentation built on March 5, 2024, 12:23 p.m.