STAR.index {ORFik} | R Documentation |
Used as reference when aligning data
Get genome and gtf by running getGenomeAndFasta()
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 |
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 |
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. |
Can only run on unix systems (Linux and Mac), and requires minimum 30GB memory on genomes like human, rat, zebrafish etc.
output.dir, can be used as as input for STAR.align..
Other STAR:
STAR.align.folder()
,
STAR.align.single()
,
STAR.install()
,
STAR.multiQC()
,
STAR.remove.crashed.genome()
,
getGenomeAndAnnotation()
,
install.fastp()
## 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)