star.command.make: generate command for STAR aligner

In VladaMilch/pdProbeRemap: What the package does (short line)

Description

make command for STAR aligner

Usage

star.command.make(path_to_STAR, sequence_fasta, genomeDir, organism, outfile,
  runThreadN = 6)

Arguments

path_to_STAR	path to STAR aligner
sequence_fasta	path to FASTA file with probe sequences (most likely, you will have to run alignment on a cluster, and copy the file from you local machine to the cluster)
genomeDir	path to reference genome annotation, build for STAR
organism	character, "Human", "Mouse" or "Dmel". Note! STAR parameters differ for Drosophila!
outfile	outFileNamePrefix, add a dot in the end.
runThreadN	outBAMsortingThreadN in STAR, 6 by default

Details

Provides a set of STAR parameters to make alignment for the probes, and returns a bash command as a character string. Needed mostly because alignments are run on clusters, but not local machines.

Value

returns a character, STAR command

Author(s)

Vladislava Milchevskaya [e-mail]

Examples

path_to_STAR = "/path/to/STAR"
sequence_fasta = "/path/to/sequence.fasta"
genomeDir = "/path/to/reference/genome/"
organism = "Human"
outfile = "output_file."
star.command.make(path_to_STAR, sequence_fasta, genomeDir, organism, outfile)

VladaMilch/pdProbeRemap documentation built on May 28, 2019, 3:21 p.m.