STAR.remove.crashed.genome {ORFik} | R Documentation

## 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"))

[Package ORFik version 1.12.13 Index]