STAR.index: Create STAR genome index
In Roleren/ORFik: Open Reading Frames in Genomics

STAR.index

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, BiocParallel::bpparam()$workers),
  max.ram = 30,
  SAsparse = 1,
  tmpDirStar = "-",
  wait = TRUE,
  remake = FALSE,
  script = system.file("STAR_Aligner", "STAR_MAKE_INDEX.sh", package = "ORFik"),
  notify_load_existing = TRUE
)

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", "contaminants", "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, BiocParallel:::bpparam()$workers)`, number of threads to use. Default is minimum of 90 and maximum cores - 2. So if you have 8 cores it will use 6. Note: FASTP will use maximum 16 threads as from testing I see performance actually degrades using anything higher. From testing I also see STAR gets no performance gain after ~50 threads. I do suspect this will change when hard drives gets better in the future.
`max.ram`	integer, default 30, in Giga Bytes (GB). Maximum amount of RAM allowed for STAR limitGenomeGenerateRAM argument. RULE: idealy 10x genome size, but do not set too close to machine limit. Default fits well for human genome size (3 GB * 10 = 30 GB)
`SAsparse`	int > 0, default 1. If you do not have at least 64GB RAM, you might need to set this to 2. suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction. Only applies to genome, not conaminants.
`tmpDirStar`	character, default "-". STAR automatic temp folder creation, deleted when done. The directory can not exists, as a safety STAR must make it!. If you are on a NFS file share drive, and you have a non NFS tmp dir, set this to `tempfile()` or the manually specified folder to get a considerable speedup!
`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.
`notify_load_existing`	logical, default TRUE. If annotation exists (defined as: locally (a file called outputs.rds) exists in outputdir), print a small message notifying the user it is not redownloading. Set to FALSE, if this is not wanted

Details

Can only run on unix systems (Linux and Mac), and requires minimum 30GB memory on genomes like human, rat, zebrafish etc.
If for some reason the internal STAR index bash script will not work for you, like if you have a very small genome. You can copy the internal index script, edit it and give that as the Index script used for this function. It is recommended to run through the RStudio local job tab, to give full info about the run. The system console will not stall, as can happen in happen in normal RStudio console.

Value

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

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)

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.