STAR.remove.crashed.genome: Remove crashed STAR genome

In JokingHero/ORFik: Open Reading Frames in Genomics

Remove crashed STAR genome

Description

This happens if you abort STAR run early, and it halts at: ..... loading genome

Usage

STAR.remove.crashed.genome(index.path, star.path = STAR.install())

Arguments

index.path	path to index folder of genome
star.path	path to STAR, default: STAR.install(), if you don't have STAR installed at default location, it will install it there, set path to a runnable star if you already have it.

Value

return value from system call, 0 if all good.

See Also

Other STAR: STAR.align.folder(), STAR.align.single(), STAR.allsteps.multiQC(), STAR.index(), STAR.install(), STAR.multiQC(), getGenomeAndAnnotation(), install.fastp()

Examples

index.path = "/home/data/human_GRCh38/STAR_INDEX/genomeDir/"
# STAR.remove.crashed.genome(index.path = index.path)
## If you have the index argument from STAR.index function:
# index.path <- STAR.index()
# STAR.remove.crashed.genome(file.path(index.path, "genomeDir"))
# STAR.remove.crashed.genome(file.path(index.path, "contaminants_genomeDir"))

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.