Run STAR on Downloaded FASTQ Files.

Run STAR on Downloaded FASTQ Files.

Usage

RunSTAR(
  sample.dir,
  ref,
  out.folder = NULL,
  thread = 4,
  star.path = NULL,
  star.paras = "--outBAMsortingThreadN 4 --twopassMode None"
)

Arguments

sample.dir

Directory contains all samples.

ref

Path of folder containing STAR version-compatible reference.

out.folder

Output folder. Default: NULL (current working directory).

thread

The number of threads to use. Default: 4.

star.path

Path to STAR. Default: NULL (conduct automatic detection).

star.paras

Parameters for STAR. Default: "--outBAMsortingThreadN 4 --twopassMode None".

Value

Vector contains failed samples or NULL.

Examples

if (FALSE) {
RunSTAR(
  sample.dir = "/path/to/fastq",
  ref = "/path/to/star/index",
  out.folder = "/path/to/star/mapping",
  star.path = "/path/to/bin/STAR"
)
}