get_genome_fasta {ORFik} | R Documentation

## Download genome (fasta), annotation (GTF) and contaminants

### Description

This function automatically downloads (if files not already exists) genomes and contaminants specified for genome alignment. Will create a R transcript database (TxDb object) from the annotation.
It will also index the genome for you
If you misspelled something or crashed, delete wrong files and run again.
Do remake = TRUE, to do it all over again.

### Usage

    get_genome_fasta(genome, output.dir, organism, assembly_type, db, gunzip)

### Arguments

`genome` | logical, default: TRUE, download genome of organism specified in "organism" argument. If FALSE, check if the downloaded file already exist. If you want to use a custom gtf from you hard drive, set GTF = FALSE, and assign: annotation <- getGenomeAndAnnotation(genome = FALSE) annotation["genome"] = "path/to/genome.fasta". Will download the primary assembly for ensembl
`output.dir` | directory to save downloaded data
`organism` | scientific name of organism, Homo sapiens, Danio rerio, Mus musculus, etc. See `biomartr:::get.ensembl.info()` for full list of supported organisms.
`assembly_type` | a character string specifying from which assembly type the genome shall be retrieved from (ensembl only, else this argument is ignored): Default is `assembly_type = "primary_assembly")`. This will give you all no copies of any chromosomes. As an example, the primary_assembly fasta genome in human is only a few GB uncompressed. `assembly_type = "toplevel")`. This will give you all multi-chromosomes (copies of the same chromosome with small variations). As an example the toplevel fasta genome in human is over 70 GB uncompressed. To get primary assembly with 1 chromosome variant per chromosome:
`db` | database to use for genome and GTF, default adviced: "ensembl" (will contain haplotypes, large file!). Alternatives: "refseq" (primary assembly) and "genbank" (mix)
`gunzip` | logical, default TRUE, uncompress downloaded files that are zipped when downloaded, should be TRUE!

### Details

If you want custom genome or gtf from you hard drive, assign it after you run this function, like this:
annotation <- getGenomeAndAnnotation(GTF = FALSE, genome = FALSE)
annotation["genome"] = "path/to/genome.fasta"
annotation["gtf"] = "path/to/gtf.gtf"

### Value

a named character vector of path to genomes and gtf downloaded, and additional contaminants if used. If merge_contaminants is TRUE, will not give individual fasta files to contaminants, but only the merged one.

### See Also

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

### Examples

    output.dir <- "/Bio_data/references/zebrafish"
    #getGenomeAndAnnotation("Danio rerio", output.dir)

    ## Get Phix contamints to deplete during alignment
    #getGenomeAndAnnotation("Danio rerio", output.dir, phix = TRUE)

[Package ORFik version 1.10.13 Index]