star: A flowr wrapper for STAR aligner

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

For more details refer to STAR's manual. Starting 2.4.2a, star supports a twoPass mode, thus simplifying this pipeline.

Usage

star.2.4.2a

star(fq1, fq2, bam,
 samplename = "samp1", out_path, out_prefix,
 ref_fasta = opts_flow$get("ref_fasta"), ref_star = opts_flow$get("ref_star"),
 star_exe = opts_flow$get("star_exe"), star_opts = opts_flow$get("star_opts"),
 star_cpu = opts_flow$get("star_cpu"))

Arguments

fq1	single fastq file
fq2	second read fastq file
bam	alternatively use of bam as input, instead of fqs
samplename	name of the sample
out_path	output path
out_prefix	output prefix
ref_fasta	path to reference genome in fasta format
ref_star	path to star's reference index
star_exe	path to star executable
star_opts	additional options passed onto star. This is a simple character vector appended to the commandline.
star_cpu	a integer specifying the number of cores to be used

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.