build.star.idx: STAR

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run STAR (runMode genomeGenerate)

Usage

build.star.idx(star.idx.dir=file.path(reference.dir, "STAR.idx"), sample.name, align.dir, ref.fa, ref.gtf, sjdbOverhang=100, star_thread_number=8, fasta.idx=TRUE, SJ.idx=FALSE, run.cmd=TRUE)

Arguments

star.idx.dir	Directory of STAR index files
sample.name	A character vector for the sample names
ref.fa	Reference fasta file path
ref.gtf	Reference gtf file path (e.g., gencode.gtf)
sjdbOverhang	A parameter value for the –sjdbOverhang in STAR. Length of the donor/acceptor sequence on each side of the junctions, ideally=(mate_length-1) (default=100)
fasta.idx	Indexing reference fasta file (when first indexing => TRUE)
SJ.idx	Indexing splicing junction (when second indexing => TRUE)
run.cmd	Whether to execute the command line (default=TRUE)
star_thread_number	A parameter value for –runThreadN in STAR. A numeric value of the number of threads (default: 8)

Details

Indexing reference fasta file and splicing junction site from fastq files.

Value

STAR reference and splicing junction indexing

References

STAR: ultrafast universal RNA-seq aligner

See Also

{https://github.com/alexdobin/STAR

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.