STAR: STAR

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

Description

A wrapper function to run STAR.

Usage

STAR(STAR.idx, fq1, fq2, sample.name, output.dir, run.cmd=TRUE, mc.cores=1)

Arguments

star.idx.dir	Directory of STAR index
output.dir	Output directory
sample.name	A character vector for the sample names
fq1	path to read1 fastq files
fq2	path to read2 fastq files
outFilterMultimapScoreRange	A parameter value for –outFilterMultimapScoreRange in STAR. The score range below the maximum score for multimapping alignments (default: 1)
outFilterMultimapNmax	A parameter value for –outFilterMultimapNmax in STAR. Read alignments will be output only if the read maps fewer than this value, otherwise no alignments will be output (default: 20)
outFilterMismatchNmax	A parameter value for –outFilterMismatchNmax in STAR. Alignment will be output only if it has fewer mismatches than this value (default: 10)
alignIntronMax	A parameter value for –alignIntronMax in STAR. Maximum intron length (default: 500,000)
alignMatesGapMax	A parameter value for –alignMatesGapMax in STAR. Maximum genomic distance between mates (default: 1,000,000)
sjdbScore	A parameter value for –sjdbScore in STAR. Extra alignment score for alignmets that cross database junctions (default: 2)
alignSJDBoverhangMin	A parameter value for –alignSJDBoverhangMin in STAR. Minimum overhang for annotated junctions (default: 1)
outFilterMatchNminOverLread	A parameter value for –outFilterMatchNminOverLread in STAR. Float: outFilterMatchNmin normalized to read length (sum of mates’ lengths for paired-end reads) (default: 0.33)
outFilterScoreMinOverLread	A parameter value for –outFilterScoreMinOverLread in STAR. Float: outFilterScoreMin normalized to read length (sum of mates’ lengths for paired-end reads) (default: 0.33)
sjdbOverhang	A parameter value for –sjdbOverhang in STAR. >=0: Length of the donor/acceptor sequence on each side of the junctions, if =0, splice junction database is not used (default: 100)
SJ.detect	First align, detection of splicing junction (default=TRUE)
SJ.align	Second align, mapping reads to fastq files (default=FALSE)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
star_thread_number	A parameter value for –runThreadN in STAR. A numeric value of the number of threads (default: 8)

Details

Spliced Transcripts Alignment to a Reference (STAR), which was designed to specifically address many of the challenges of RNA-seq data mapping, and uses a novel strategy for spliced alignments.

Value

Aligned BAM files

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.