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.
`db` | database to use for genome and GTF, default adviced: "ensembl" (remember to set assembly_type to "primary_assembly", else it will contain haplotypes, very 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

    ## Get Saccharomyces cerevisiae genome and gtf (create txdb for R)
    #getGenomeAndAnnotation("Saccharomyces cerevisiae", tempdir(), assembly_type = "toplevel")
    ## Get Danio rerio genome and gtf (create txdb for R)
    #getGenomeAndAnnotation("Danio rerio", tempdir())

    output.dir <- "/Bio_data/references/zebrafish"
    ## Get Danio rerio and Phix contamints to deplete during alignment
    #getGenomeAndAnnotation("Danio rerio", output.dir, phix = TRUE)

    ## Optimize for ORFik (speed up for large annotations like human or zebrafish)
    #getGenomeAndAnnotation("Danio rerio", tempdir(), optimize = TRUE)

    ## How to save malformed refseq gffs:
    ## First run function and let it crash:
    #annotation <- getGenomeAndAnnotation(organism = "Arabidopsis thaliana", output.dir = "~/Desktop/test_plant/",
    #  assembly_type = "primary_assembly", db = "refseq")
    ## Then apply a fix (example for linux, too long rows):
    # \code{system("cat ~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.gff | awk '{ if (length($0) < 32768) print }' > ~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq_trimmed2.gff")}
    ## Then updated arguments:
    annotation <- c("~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq_trimmed.gff",
     "~/Desktop/test_plant/Arabidopsis_thaliana_genomic_refseq.fna")
    names(annotation) <- c("gtf", "genome")
    # Make the txdb (for faster R use)
    # makeTxdbFromGenome(annotation["gtf"], annotation["genome"], organism = "Arabidopsis thaliana")

[Package ORFik version 1.12.13 Index]