STAR.index {ORFik} | R Documentation

## Create STAR genome index

### Description

Used as reference when aligning data
Get genome and gtf by running getGenomeAndFasta()

### Usage

    STAR.index(
      arguments,
      output.dir = paste0(dirname(arguments[1]), "/STAR_index/"),
      star.path = STAR.install(),
      max.cpus = min(90, detectCores() - 1),
      wait = TRUE,
      remake = FALSE,
      script = system.file("STAR_Aligner", "STAR_MAKE_INDEX.sh", package = "ORFik")
    )

### Arguments

`arguments` | a named character vector containing paths wanted to use for index creation. They must be named correctly: names must be a subset of: c("gtf", "genome", "phix", "rRNA", "tRNA","ncRNA")
`output.dir` | directory to save indices, default: paste0(dirname(arguments[1]), "/STAR_index/"), where arguments is the arguments input for this function.
`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.
`max.cpus` | integer, default: min(90, detectCores() - 1), number of threads to use. Default is minimum of 90 and maximum cores - 1
`wait` | a logical (not `NA`) indicating whether the R interpreter should wait for the command to finish, or run it asynchronously. This will be ignored (and the interpreter will always wait) if `intern = TRUE`. When running the command asynchronously, no output will be displayed on the `Rgui` console in Windows (it will be dropped, instead).
`remake` | logical, default: FALSE, if TRUE remake everything specified
`script` | location of STAR index script, default internal ORFik file. You can change it and give your own if you need special alignments.

### Details

Can only run on unix systems (Linux and Mac), and requires minimum 30GB memory on genomes like human, rat, zebrafish etc.

### Value

output.dir, can be used as as input for STAR.align..

### See Also

Other STAR: `STAR.align.folder()`, `STAR.align.single()`, `STAR.install()`, `STAR.multiQC()`, `STAR.remove.crashed.genome()`, `getGenomeAndAnnotation()`, `install.fastp()`

### Examples

    ## Manual way, specify all paths yourself.
    #arguments <- c(path.GTF, path.genome, path.phix, path.rrna, path.trna, path.ncrna)
    #names(arguments) <- c("gtf", "genome", "phix", "rRNA", "tRNA","ncRNA")
    #STAR.index(arguments, "output.dir")

    ## Or use ORFik way:
    output.dir <- "/Bio_data/references/Human"
    # arguments <- getGenomeAndAnnotation("Homo sapiens", output.dir)
    # STAR.index(arguments, output.dir)

[Package ORFik version 1.8.6 Index]